Calibrated Similarity for Reliable Geometric Analysis of Embedding Spaces

Abstract: While raw cosine similarity in pretrained embedding spaces exhibits strong rank correlation with human judgments, anisotropy induces systematic miscalibration of absolute values: scores concentrate in a narrow high-similarity band regardless of actual semantic relatedness, limiting interpretability as a quantitative measure. Prior work addresses this by modifying the embedding space (whitening, contrastive fine tuning), but such transformations alter geometric structure and require recomputing all embeddings. Using isotonic regression trained on human similarity judgments, we construct a monotonic transformation that achieves near-perfect calibration while preserving rank correlation and local stability(98% across seven perturbation types). Our contribution is not to replace cosine similarity, but to restore interpretability of its absolute values through monotone calibration, without altering its ranking properties. We characterize isotonic calibration as an order-preserving reparameterization and prove that all order-based constructions (angular ordering, nearest neighbors, threshold graphs and quantile-based decisions) are invariant under this transformation.