Foundation models are used to extract transferable representations from large amounts of unlabeled data, typically via self-supervised learning (SSL). However, many of these models rely on architectures that offer limited interpretability, a critical issue in high-stakes domains such as medical imaging. We propose \model, a foundation model that is interpretable-by-design via a BagNet backbone whose small receptive fields generate class evidence maps that are faithful to the model's decision-making process. Additionally, \model{} incorporates a 2D projection layer during pretraining that enables direct visualization of the representation space, providing a dataset-level view of the learned structure including meaningful clinical clusters as well as potential spurious correlations. We trained \model{} on over 800,000 color fundus photographs from various sources to learn generalizable representations for different downstream tasks. Our model achieves performance comparable to RETFound, which has 16× more parameters, while providing interpretable predictions on out-of-distribution data. These results suggest that large-scale SSL pretraining paired with inherent interpretability can lead to robust representations for retinal imaging. Code and pretrained models are available at \href{https://anonymous.4open.science/r/dual-ifm-3D5A/README.md}{www.anonymous.4open.science/dual-IFM}.
Despite the widespread adoption of foundation models as feature extractors for medical imaging, relatively little is understood about how different pretraining strategies influence the transferability of learned representations to weakly supervised ophthalmic imaging tasks. We investigate this question in ultra-widefield (UWF) retinal imaging by evaluating foundation model representations within a patch-based multiple instance learning (MIL) framework for disease classification on UWF images. We compare Vision Transformer encoders pretrained with supervised, Masked Autoencoder (MAE), and self-distillation objectives, while keeping the downstream aggregation architecture unchanged. Within a controlled comparison of ViT-B encoders pretrained on ImageNet-1k, the choice of pretraining objective substantially influenced frozen representation transfer, with supervised and self-distillation-based models outperforming MAE. A contemporary DINOv3 model pretrained at a larger scale achieved the strongest overall performance, with a quadratic weighted kappa of 0.863 for five-class diabetic retinopathy grading, comparable with DINOv1. Attention analysis further revealed distinct patch-aggregation behaviours associated with the different pretrained representations, while partial fine-tuning substantially reduced the performance gap for MAE. These findings suggest that pretraining strategy influences both representation transferability and the subsequent aggregation of patch-level evidence within MIL, resulting in differences in downstream classification performance.
Mingya Alexa Gong, Da Ma, Lovre Antonio Budimir +7
Medical foundation models learn latent representations of clinically meaningful phenotypes, yet their ability to support controllable image generation remains largely unexplored. We evaluate four retinal foundation models within the representation tokenizer framework and examine whether demographic and clinical information encoded in latent representations from foundation models is preserved during synthetic image generation. We show that generated representations and images faithfully inherit phenotype information when evaluated within their originating foundation models, consistently outperforming conventional latent diffusion on multiple downstream prediction tasks. However, these gains largely disappear when evaluated using classifiers trained on real images, revealing a previously uncharacterised synthetic-to-real representation gap. These findings demonstrate that foundation-model latent spaces provide a powerful substrate for controllable retinal synthesis while highlighting the need to better align synthetic representations with real-image distributions.
Zuzanna A. Wakefield-Skórniewska, Bartłomiej W. Papież
Color fundus photography (CFP) is the mainstay of large-scale retinal screening, but its diagnostic capacity is limited by the lack of depth-resolved structure, which optical coherence tomography (OCT) provides yet is less accessible at population scale. We present EyeMVP, a cross-modal retinal foundation model that uses paired CFP--OCT pretraining to learn OCT-informed CFP representations while requiring only CFP at inference. Pretrained on 674,893 same-eye same-day CFP--OCT triples from 112,642 patients across eight hospitals, EyeMVP uses cross-modal masked reconstruction to enrich CFP features with OCT-associated supervision, and combines source-constrained cross-attention with CFP-derived structural masks to accommodate the non-aligned geometry of en-face CFP and cross-sectional OCT. Across 15 dataset-level settings spanning classification and segmentation, under both full-data and few-shot regimes, EyeMVP performs on par with or better than representative retinal foundation models, with consistent gains on macular and optic-nerve tasks; it attains AUROCs of 0.923 for macular edema and 0.867 for myopic macular schisis, two conditions poorly resolved in CFP. In an exploratory reader study, EyeMVP surpasses junior and intermediate ophthalmologists but not seniors on macular edema, while exceeding all groups on myopic macular schisis. These results indicate that cross-modal reconstruction can enrich CFP representations with OCT-associated supervision, offering a practical route to stronger CFP-based screening.