Active Spatial Guidance: Eliminating Injected Positional Mechanisms in Vision Transformers

Vision Transformers trained only on image classification routinely transfer to tasks that demand spatial understanding, yet they receive no spatial supervision during pretraining. We ask where and how robustly such structure is encoded. Probing a frozen ViT-B/16 layerwise for two complementary properties, local patch boundaries (BSDS500) and per-patch depth (NYU Depth V2), reveals a clear hierarchy: boundary structure becomes linearly decodable at layers 5-6 (AP = 0.833), while depth, which requires integrating global cues, peaks two to three layers later at layer 8 (MAE = 0.0875). Both signals collapse at the final classification layer, and random-weight controls confirm the encodings are learned rather than architectural. Causal interventions add specificity: ablating the single direction a linear depth probe reads degrades depth decoding by up to 165%, while ablating any other direction changes it by less than 1%. Targeted activation patching along that direction shows the depth signal is partially re-derived at each layer rather than passively carried in the residual stream, with mid-layer interventions persisting most strongly downstream. The result is that a classification-trained ViT develops an actively maintained spatial hierarchy that mirrors the early-to-late progression observed in the primate visual cortex.

Positional embeddings (PEs) in Vision Transformers (ViTs) are known to impact performance and robustness, but their role in shaping internal spatial representations is not well understood. In this work, we study how different forms of PEs influence the representational geometry of ViTs and how these changes relate to robustness under content-disrupting distribution shifts. We introduce a metric, the Spatial Similarity Distance Correlation (SSDC), to quantify spatial structure in token representations. Using this metric, we show that ViTs trained without PEs still develop non-trivial spatial structure, but this structure is driven by visual content and collapses under token permutation. In contrast, we find that all PEs considered (learned absolute, sinusoidal, and rotary) are associated with a consistent shift toward an index-anchored spatial organization. Representations in these models remain stable under perturbations that disrupt content, and exhibit substantially improved robustness to such distributional shifts. We further show that while different PEs produce distinct depth-wise trajectories of spatial structure, their robustness properties are largely similar (with secondary variation across encoding schemes), suggesting that robustness appears to depend on the presence of a stable positional reference frame more than it depends on the specific encoding mechanism. These results offer a geometric account of how positional encodings shape internal representations, with implications for the principled design of future encoding schemes.

Representation learning with Vision Transformers (ViTs) has advanced rapidly, yet the utility of large-scale models in spatially sensitive tasks is hindered by spurious tokens. Prior efforts to mitigate this have been limited, often defining these artifacts narrowly, for example, as simple high-norm outliers. We argue that this scope is insufficient. For dense prediction tasks, we posit that any token failing to encode location-aligned semantics should be treated as a spurious artifact. This broader definition reveals a more complex problem, leading us to systematically categorize and characterize three fundamental types of spurious tokens that corrupt spatial representations. Based on this comprehensive diagnosis, we propose UniRefiner, a universal refinement framework that teaches pre-trained ViTs to self-dispose of these artifacts. UniRefiner uses contrastive registers to explicitly isolate and redistribute spurious tokens via a dual objective: (i) it aligns image tokens with filtered regular tokens to preserve semantics, and (ii) it aligns register tokens with detected spurious tokens to capture the spurious signals. Our method requires only a few epochs of fine-tuning on ~5k images to refine diverse ViTs, including massive models like EVA-CLIP-8B and InternViT-6B. Experiments demonstrate consistent and significant improvements: notably, the refined EVA-CLIP-8B achieves 51.9% mIoU on ADE20K (+9.4%), surpassing specialized vision models like DINOv2 (49.1%), while zero-shot segmentation accuracy improves by up to 22%. UniRefiner unlocks the latent spatial potential of existing large-scale foundation models, paving the way for their broader application.