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Life sciences · Preprint
arXiv · October 26, 2026
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Computing local-level variable importance (VI) is critical for understanding machine learning models. Local permutation-based VI metrics offer a simple yet powerful approach, measuring how much a model's output changes when perturbing its inputs. However, existing perturbation strategies often ignore feature dependence or account for it only through restricted approximations. Perturbing a feature without fully respecting this dependence can generate unrealistic counterfactuals, thereby evaluating the model in regions unsupported by the observed data distribution. We address this gap by introducing a new model-agnostic local VI metric and estimator, Local Understanding of Covariate Importance with conditional Density estimation (LUCID). LUCID perturbs features of interest using plausible values drawn from the full conditional distribution given the remaining observed features. We establish theoretical connections between LUCID and existing VI measures, and provide an estimator with convergence guarantees and uncertainty quantification. Finally, we demonstrate LUCID's stable performance and practical utility across simulated and real-world examples.