用解剖结构解释脑MRI模型预测,让医生看得懂。
RegionFM: Interpretable Region-Based Brain MRI Classification Using Foundation Model Embeddings

- 将脑扫描按解剖区域分割,分别编码为嵌入向量
- 各区域贡献可量化,解释结果与临床解剖一致
- 保持高精度同时提供可读性解释,适合临床应用
基础模型为脑部MRI分析提供了强大的表征能力,但其预测难以用解剖学意义的语言解释。临床评估通常基于解剖定义的结构和区域异常,而传统解释方法多生成体素或图像块级重要性图,无法明确量化各脑区的贡献。为此,我们提出RegionFM,一种结合解剖分割与脑部MRI基础模型嵌入的可解释框架。RegionFM首先将每张MRI扫描按解剖区域划分,并为每个区域构建独立的影像体积;使用冻结的基础模型对每个区域编码为嵌入向量,再通过区域加性逻辑回归模型融合这些嵌入,使每个解剖区域在最终预测中贡献一个明确的标量项。该设计支持个体和群体层面的区域贡献分析。我们在多个预训练脑部MRI基础模型嵌入上,针对认知功能障碍分类任务评估RegionFM。结果表明,RegionFM在保持与微调方法相当的性能的同时,提供解剖学意义上的解释。随机嵌入消融实验表现接近随机水平,说明预测依赖于基础模型捕捉到的有意义结构,而非简单特征统计。总体而言,RegionFM更契合基于解剖的临床推理方式,同时维持了具有竞争力的预测性能。
原文摘要 · Abstract (English)
Foundation models provide powerful representations for brain MRI analysis, but their predictions remain difficult to interpret in anatomically meaningful terms. Clinical assessment of brain MRI is commonly organized around anatomically defined structures and regional abnormalities, whereas conventional explanation methods typically produce voxel- or patch-level importance maps that do not explicitly quantify the contributions of individual brain regions. To address this mismatch, we propose RegionFM, an interpretable framework that integrates anatomical segmentation with brain MRI foundation-model embeddings. RegionFM first divides each MRI scan into anatomical regions and constructs a separate MRI volume for each region. A frozen foundation model then encodes each region into an embedding, and a region-additive logistic model combines these embeddings such that every anatomical region contributes an explicit scalar term to the final prediction. This formulation supports both subject-level and cohort-level analyses of regional contributions. We evaluate RegionFM on cognitive-impairment classification using embeddings from multiple pretrained brain MRI foundation models. The results show that RegionFM maintains performance comparable to less interpretable fine-tuning approaches while providing anatomically grounded explanations. Randomized embedding ablations yield near-chance performance, indicating that the predictions rely on meaningful structure captured by the foundation-model embeddings rather than simple feature statistics. Overall, RegionFM better aligns model explanations with anatomy-based clinical reasoning while maintaining competitive predictive performance.
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