Frozen Vision Transformers for Dense Prediction on Small Datasets: A Case Study in Arrow Localization

Frozen vision-transformer (ViT) foundation-model embeddings increasingly serve as the substrate for downstream chest-radiography (CXR) pipelines, yet where small-scale, low-contrast signal is retained or lost in the frozen forward pass has not been systematically quantified across architectures, pretraining domains, and objectives. We probed five frozen ViTs (RAD-DINO, DINOv2-B/14, DINOv3 ViT-7B, BiomedCLIP, MedSigLIP) and a frozen DINO-pretrained ResNet-50 architectural control across three large CXR cohorts (NIH-CXR14, MIMIC-CXR, Emory-CXR; aggregate pool n=492,724) and ChestX-Det10 (n=3,543; 1,462 small-lesion bounding boxes across Calcification, Nodule, Mass). Each model was evaluated with a small-scale-perturbation panel and a region-aware bounding-box-stratified probe on real lesions, comparing three pooling modes from the same forward pass: classification token (CLS), patch-mean (mean over all final-layer patch tokens), and bounding-box-restricted patch-local. On the perturbation panel, CLS embeddings sat at the chance floor (area under the ROC curve [AUC] 0.500-0.524); patch-mean was indistinguishable from CLS on iso-blur and reticular-fine cells but rose with CLS on larger directional-blur footprints, while disease AUC on globally decided tasks ranged 0.642-0.913. Patch-local probes recovered AUC ~1.0 from the same forward pass (per-model mean improvement +0.412 to +0.488); the ResNet-50 control reproduced the chance floor. On ChestX-Det10, image-level CLS classification showed within-class small-versus-large stratum gaps up to +0.243 AUC; bounding-box-level patch-local pooling on the same forward pass recovered AUC >= 0.899 on every (model x class) cell. Frozen ViT embeddings silently suppress small-scale signal at the global-aggregation step; the signal is recoverable from patch tokens conditional on a region of interest.

Although large-scale visual foundation models (VFMs) achieve remarkable performance in semantic understanding, they still underperform in instance-aware dense prediction tasks. They exhibit different biases in representation: for instance, promptable segmentation models (e.g., SAM2) focus on fine-grained region boundaries, while self-supervised models (e.g., DINOv3) emphasize object-level structure. This observation highlights the potential of combining complementary features from different VFMs to enhance downstream dense prediction tasks. However, naive multi-VFM fusion seldom leads to reliable gains, and interpretable principles for leveraging their complementary features are still underexplored. In this work, we propose a metric-guided approach that effectively selects and aggregates complementary features from different VFMs based on explicit assessment scores. Specifically, we design a suite of label-free metrics in feature space across two aspects, Structural Coherence and Edge Fidelity, to assess features of VFM encoders. Guided by these scores, we identify complementary edge-strong and structure-strong encoder pairs, and integrate them via a master-auxiliary fusion scheme. This feature fusion requires no complex architectural changes and is trained only in a single stage. Our model shows consistent performance gains across multiple dense prediction tasks compared with the baselines, with better object-level semantics and more accurately localized boundaries. The code is available at {https://github.com/gyc-code/metric-guided-fusion}.

Frozen Vision Foundation Models (VFMs) with lightweight classification heads are increasingly used in medical imaging because they offer efficient and reproducible deployment. Yet noisy-label learning methods for this frozen-feature regime remain poorly understood, and most existing methods still rely on a small-loss assumption inherited from end-to-end training. We present a controlled benchmark of eight noisy-label methods across five medical datasets, three backbones, two noise types, and five noise rates (150 conditions, 6,000 training runs), evaluated with balanced accuracy. The benchmark shows that there is no universal winner: Friedman ranking over the 150 conditions yields $χ^2 = 333.2$ ($p = 4.77 \times 10^{-68}$), ELR wins the most conditions (49/150), while CUFIT attains the best mean rank (2.51). The practical cost of method choice grows sharply with noise severity, from 4.5pp on clean data to 18.8pp at asymmetric 40% noise. To explain these benchmark-level patterns, we revisit the small-loss assumption in a representative high-risk regime. Under frozen DINOv2 features, clean and noisy loss distributions overlap by 53--61%, and matched-rate clean-sample detection shows that prediction agreement is markedly more stable than loss ranking under asymmetric noise (3pp vs.\ 13pp precision drop). On ISIC2019 with asymmetric 40% noise, Co-Teaching reaches 68% overall accuracy while collapsing to 35.1% balanced accuracy with zero recall on three minority classes. Together, these results recast noisy-label learning for frozen VFMs as a regime-aware method-selection problem rather than a search for a single dominant algorithm. We conclude with evidence-based guidance and a low-regret feature-space selector for practical recommendation.