Counterfactual Explanations for Graph Neural Networks in Patient Outcome Prediction
Journal:
bioRxiv
Published Date:
May 20, 2026
Abstract
Counterfactual Explanation (CE) algorithms have been successfully applied to uncover the main factors driving computational diagnostic and prognostic predictions on tabular medical data.Recently, a new Network Medicine paradigm has been introduced for patient diagnosis and prognosis using Patient Similarity Networks (PSNs), i.e. graphs where patients are represented as nodes and their clinical and biomolecular similarities as edges. In this context, graph-based algorithms, including Graph Neural Networks (GNNs), can provide predictions using not only individual patient features but also their relations within a network of clinically and biomolecularly similar individuals. In this work, we propose the first CE algorithm tailored to explain diagnostic and prognostic predictions within PSNs. Alongside a contrastive GNN backbone, we introduce a versatile, model-agnostic counterfactual search method compatible with any underlying classifier. Preliminary results on synthetic data and on a cohort of patients affected by the Alzheimer's disease show that our algorithm is competitive both with seminal tabular based CE algorithms and GNNExplainer, a well-established method for explaining graph-based classification tasks.
