Hierarchical Perfusion Graphs for Tumor Heterogeneity Modeling in Glioma Molecular Subtyping
This work addresses the need for non-invasive glioma molecular subtyping to guide surgical and therapeutic decisions, offering a robust method that leverages perfusion data to overcome limitations of anatomy-only approaches.
HiPerfGNN integrates perfusion MRI dynamics with structural MRI via a hierarchical graph neural network to non-invasively predict glioma molecular subtypes, achieving AUCs of 0.96 for IDH, 0.89 for 1p/19q, and 0.84 for WHO grade on an internal cohort (n=475), with robust IDH performance (AUC 0.89) on an external cohort (n=397).
Precise molecular subtyping of gliomas, including isocitrate dehydrogenase (IDH) mutation and 1p/19q codeletion, directly guides surgical and therapeutic decisions, yet currently relies on invasive tissue sampling. Deep learning on structural MRI has emerged as a non-invasive alternative, but anatomy-only approaches cannot capture the hemodynamic signatures that distinguish molecular subtypes. Radiogenomics based on dynamic susceptibility contrast (DSC) MRI holds immense potential for non-invasively characterizing glioma molecular subtypes, yet clinical deployment has been hindered by inter-site variability and the limitations of voxel-wise analysis. We introduce HiPerfGNN, a framework that first learns discrete hemodynamic representations from raw time-intensity curves using a vector-quantized variational autoencoder (VQ-VAE). These quantized perfusion codes define coarse-level graph nodes representing functional tumor habitats, each of which is hierarchically subdivided into fine-level subregions guided by structural MRI. A hierarchical graph neural network then propagates information across scales for molecular prediction. On an internal cohort (n=475), the model achieved AUCs of 0.96 (IDH), 0.89 (1p/19q), and 0.84 (WHO grade), and maintained robust IDH performance (AUC 0.89) on an independent external cohort (n=397) without recalibration. Gradient-based saliency analysis confirms biologically grounded attention patterns aligned with known glioma pathophysiology. Our results demonstrate the added value of integrating perfusion dynamics into radiogenomic pipelines for glioma molecular subtyping. Code is available at https://github.com/janghana/HiPerfGNN.