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

arXiv: https://arxiv.org/abs/2508.14482 · HTML: https://mlsanity.com/paper/2508.14482/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 39 of its 53 references that are in the map.
- First posted on arXiv 20 Aug 2025.

## Builds on (most cited first, 30 of 39)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Learning Important Features Through Propagating Activation Differences](https://mlsanity.com/paper/1704.02685/) (2017)
- [Swin Transformer V2: Scaling Up Capacity and Resolution](https://mlsanity.com/paper/2111.09883/) (2021)
- [Sanity Checks for Saliency Maps](https://mlsanity.com/paper/1810.03292/) (2018)
- [Explaining Machine Learning Classifiers through Diverse Counterfactual Explanations](https://mlsanity.com/paper/1905.07697/) (2019)
- [Interpretable Explanations of Black Boxes by Meaningful Perturbation](https://mlsanity.com/paper/1704.03296/) (2017)
- [A Benchmark for Interpretability Methods in Deep Neural Networks](https://mlsanity.com/paper/1806.10758/) (2018)
- [Interpretation of Neural Networks is Fragile](https://mlsanity.com/paper/1710.10547/) (2017)
- [The (Un)reliability of saliency methods](https://mlsanity.com/paper/1711.00867/) (2017)
- [On the (In)fidelity and Sensitivity for Explanations](https://mlsanity.com/paper/1901.09392/) (2019)
- [Real Time Image Saliency for Black Box Classifiers](https://mlsanity.com/paper/1705.07857/) (2017)
- [What do different evaluation metrics tell us about saliency models?](https://mlsanity.com/paper/1604.03605/) (2016)
- [Explainable artificial intelligence (XAI) in deep learning-based medical image analysis](https://mlsanity.com/paper/2107.10912/) (2021)
- [HIVE: Evaluating the Human Interpretability of Visual Explanations](https://mlsanity.com/paper/2112.03184/) (2021)
- [Guided Integrated Gradients: An Adaptive Path Method for Removing Noise](https://mlsanity.com/paper/2106.09788/) (2021)
- [Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm](https://mlsanity.com/paper/1906.03720/) (2019)
- [How do Humans Understand Explanations from Machine Learning Systems? An Evaluation of the Human-Interpretability of Explanation](https://mlsanity.com/paper/1802.00682/) (2018)
- [An Evaluation of the Human-Interpretability of Explanation](https://mlsanity.com/paper/1902.00006/) (2019)
- [A Rigorous Study of Integrated Gradients Method and Extensions to Internal Neuron Attributions](https://mlsanity.com/paper/2202.11912/) (2022)
- [GANterfactual - Counterfactual Explanations for Medical Non-Experts using Generative Adversarial Learning](https://mlsanity.com/paper/2012.11905/) (2020)
- [Visual Feature Attribution using Wasserstein GANs](https://mlsanity.com/paper/1711.08998/) (2017)
- [Fast Diffusion-Based Counterfactuals for Shortcut Removal and Generation](https://mlsanity.com/paper/2312.14223/) (2023)
- [Using StyleGAN for Visual Interpretability of Deep Learning Models on Medical Images](https://mlsanity.com/paper/2101.07563/) (2021)
- [Global and Local Interpretability for Cardiac MRI Classification](https://mlsanity.com/paper/1906.06188/) (2019)
- [Manifold Integrated Gradients: Riemannian Geometry for Feature Attribution](https://mlsanity.com/paper/2405.09800/) (2024)
- [ICAM: Interpretable Classification via Disentangled Representations and Feature Attribution Mapping](https://mlsanity.com/paper/2006.08287/) (2020)

## Abstract (arXiv)

The explainability of deep learning models remains a significant challenge, particularly in the medical domain where interpretable outputs are essential for clinical trust and transparency. Path attribution methods such as Integrated Gradients rely on a baseline that represents the absence of informative features, a notion commonly referred to as missingness. Standard baselines, such as all-zero inputs, are often semantically meaningless in medical contexts, where intensity values carry clinical significance. In this work, we revisit the notion of missingness for medical imaging, expose the limitations of standard baselines in this setting, and formalize a stricter missingness we term semantic missingness: a baseline must not merely lack signal, but must represent a clinically plausible state in which the disease-related features are absent. This formulation motivates a counterfactual-guided approach to baseline selection, in which a synthetically generated counterfactual (i.e. a clinically normal variant of the pathological input) serves as a principled and semantically meaningful reference. We derive theoretical guarantees showing that counterfactual baselines yield more faithful attributions than standard alternatives, and empirically validate this with two complementary counterfactual generative models, a VAE and a diffusion model, though the concept is model-agnostic and compatible with any suitable counterfactual method. Across three diverse medical datasets, counterfactual baselines produce more faithful and medically relevant attributions, outperforming standard baseline choices as well as related methods. Notably, we also compare against using the counterfactual directly as an explanation (an established paradigm in its own) and show that employing it as a baseline for Integrated Gradients yields superior results, thereby bridging two complementary explainability paradigms.