Do Medical Vision Models Reason About Anatomy? Probing the Spatial Inductive Biases of Learned Visual Representations

Abstract

Interpreting a CT scan means comparing structures on either side, judging how far apart organs sit, and knowing where each one belongs. Medical vision encoders are evaluated on diagnostic accuracy, or through assembled multimodal systems where a failure is hard to attribute, so it remains unclear whether their representations support any of this. We construct SPAR-Bench, eight probes over multi-organ abdominal CT that separate coordinate localization, relational reasoning, and spatial queries, and apply them to five architectural configurations and three medical foundation models, frozen and finetuned. Probes that ask for a comparison within the slice stay at chance, and neither pretraining scale, finetuning, nor architecture closes the gap. Probes that appear solved in domain fall to chance under zero-shot transfer, indicating that their accuracy reflects recall of canonical anatomy rather than computation over the image. Reading the same frozen features with a pooled head rather than the full set of tokens moves relational recovery from 0.7% to 67.8%, so pooled probing understates what a representation holds. Questions the encoders answer well are answered at chance by four open-weight MLLMs. Our results suggest these encoders carry a map of where organs usually lie, and little of the machinery for comparing structures within a particular patient. Code and data will be available at https://spar-bench.github.io.