On the notion of missingness for path attribution explainability methods in medical settings: Guiding the selection of medically meaningful baselines

The explainability of deep learning models remains a significant challenge, particularly in the medical domain where interpretable outputs are critical for clinical trust and transparency. Path attribution methods such as Integrated Gradients rely on a baseline representing the absence of relevant features ("missingness"). Commonly used baselines, such as all-zero inputs, are often semantically meaningless, especially in medical contexts. While alternative baseline choices have been explored, existing methods lack a principled approach to dynamically select baselines tailored to each input. In this work, we examine the notion of missingness in the medical context, analyze its implications for baseline selection, and introduce a counterfactual-guided approach to address the limitations of conventional baselines. We argue that a generated counterfactual (i.e. clinically "normal" variation of the pathological input) represents a more accurate representation of a meaningful absence of features. We use a Variational Autoencoder in our implementation, though our concept is model-agnostic and can be applied with any suitable counterfactual method. We evaluate our concept on three distinct medical data sets and empirically demonstrate that counterfactual baselines yield more faithful and medically relevant attributions, outperforming standard baseline choices as well as other related methods.