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Encoding Structural Constraints into Segment Anything Models via Probabilistic Graphical Models

While the Segment Anything Model (SAM) has achieved remarkable success in image segmentation, its direct application to medical imaging remains hindered by fundamental challenges, including ambiguous boundaries, insufficient modeling of anatomical relationships, and the absence of uncertainty quantification. To address these limitations, we introduce KG-SAM, a knowledge-guided framework that synergistically integrates anatomical priors with boundary refinement and uncertainty estimation. Specifically, KG-SAM incorporates (i) a medical knowledge graph to encode fine-grained anatomical relationships, (ii) an energy-based Conditional Random Field (CRF) to enforce anatomically consistent predictions, and (iii) an uncertainty-aware fusion module to enhance reliability in high-stakes clinical scenarios. Extensive experiments across multi-center medical datasets demonstrate the effectiveness of our approach: KG-SAM achieves an average Dice score of 82.69% on prostate segmentation and delivers substantial gains in abdominal segmentation, reaching 78.05% on MRI and 79.68% on CT. These results establish KG-SAM as a robust and generalizable framework for advancing medical image segmentation.