$Δ$Representation: Geometry Supervised Representation Learning of Phenotypes via Counterfactual Reasoning for Medical VLMs

Hao Wang, Qiwei Zeng, Jinghao Lin, Shuchang Ye, Yuezhe Yang +4

Medical vision-language models (VLMs) have shown increasing potential for radiological image interpretation. Medical VLMs encode radiological images into visual representations that capture both anatomical and phenotypic information for diagnosis. Existing approaches improve pathological phenotype representations through semantic-guided representation alignment. However, pathological phenotypes arise as lesion-specific visual changes superimposed on underlying normal anatomy. Such semantic alignment approaches fail to model the phenotype-specific increment relative to the corresponding normal anatomical representation. To address this gap, we propose \textbf{$Δ$Representation}, a visual phenotype representation learning framework based on counterfactual reasoning for medical VLMs. It comprises \textbf{BaseAnatomy}, a geometry-supervised representation learning module, and \textbf{$Δ$Phenotype}, a counterfactual incremental representation learning module. BaseAnatomy provides fine-grained geometric supervision through spatial relationships across and within anatomical structures. $Δ$Phenotype computes the representation increment between lesion representations and their…