An Accurate and Interpretable Hyper Graph Neural Network for GBM Survival Prediction

Abstract

Survival prediction for glioblastoma multiforme (GBM) demands models that are both accurate and interpretable, yet existing approaches treat these objectives as com- peting, where performant models sacrifice transparency, while interpretable models accept degraded predictive power. We argue that this trade-off is not inherent. Graph neural net- works offer a structural foundation for extracting interpretable, explainable representations without compromising discriminative ability. Furthermore, current methods typically rely on a single imaging modality, underutilizing the complementary information available across multi-modal MRI and clinical metadata. We propose a multi-modal framework that inte- grates three components to address both objectives simultaneously: (1) a sheaf hypergraph neural network that captures higher-order relationships among tissue patches through direc- tional, asymmetric message passing; (2) a concept bottleneck layer that compresses learned representations into clinically grounded concepts, enforcing ante-hoc interpretability; and (3) an extension sufficiency test (EST) regularizer that penalizes unfaithful explanations during training, ensuring that model explanations genuinely reflect the internal decision process. Clinical and genomic features are incorporated through gated fusion, preserving the dominant prognostic signal of molecular markers while retaining concept-level traceabil- ity. Evaluated on 593 patients from the UPenn-GBM dataset under 5-fold cross-validation, our framework achieves a concordance index of 0.643 with the lowest fold-level variance among all compared models (std = 0.015). To our knowledge, this is the first work to unify sheaf hypergraph convolution, concept bottleneck supervision, and EST regularization for interpretable survival prediction from brain MRI