Geometry-Supervised Visual Representation Learning for Multi-Phenotype Lesion Interpretation in Medical VLMs

Medical vision-language models (VLMs) have shown increasing potential for clinical image interpretation. However, these models still struggle to interpret multi-phenotype lesions whose diagnosis requires the joint assessment of multiple pathological phenotypes. Existing vision–language alignment methods produce visual representations that fail to preserve anatomical hierarchies and relationships among phenotypic subclasses. This stems from their reliance on semantic supervision, which lacks geometric constraints to preserve these relationships in the visual embedding space. Moreover, the sparsity of lesion-related anatomical and phenotypic representations makes it difficult for medical VLMs to capture important diagnostic evidence. To address these limitations, we propose PureVision, a geometry-supervised visual representation learning framework for multi-phenotype lesion interpretation in medical VLMs. It combines a geometry-supervised representation learning module, PureEyes, and an anatomy-guided evidence aggregation module, PureNeurons. PureEyes provides geometric supervision through ideal spatial distributions that encode anatomical hierarchies and phenotypic subclass relationships. PureNeurons projects visual representations into the learned latent space, using their positions to selectively aggregate lesion-specific anatomical and phenotypic evidence. Experiments on LIDC-IDRI, CBIS-DDSM, and 3DReasonKnee demonstrate that PureVision improves lesion grounding and phenotype characterization in visual question answering and radiology report generation. Code is available at: https://anonymous.4open.science/r/purevision-06C2.