We propose a novel pairwise distance measure between image keypoint sets, for the purpose of large-scale medical image indexing. Our measure generalizes the Jaccard index to account for soft set equivalence (SSE) between keypoint elements, via an adaptive kernel framework modeling uncertainty in keypoint appearance and geometry. A new kernel is proposed to quantify the variability of keypoint geometry in location and scale. Our distance measure may be estimated between $O(N^2)$ image pairs in $O(N~\log~N)$ operations via keypoint indexing. Experiments report the first results for the task of predicting family relationships from medical images, using 1010 T1-weighted MRI brain volumes of 434 families including monozygotic and dizygotic twins, siblings and half-siblings sharing 100%-25% of their polymorphic genes. Soft set equivalence and the keypoint geometry kernel improve upon standard hard set equivalence (HSE) and appearance kernels alone in predicting family relationships. Monozygotic twin identification is near 100%, and three subjects with uncertain genotyping are automatically paired with their self-reported families, the first reported practical application of image-based family identification. Our distance measure can also be used to predict group categories, sex is predicted with an AUC=0.97. Software is provided for efficient fine-grained curation of large, generic image datasets.