Lymph Node Graph Neural Networks for Cancer Metastasis Prediction

3 Jun 2021  ·  Michal Kazmierski, Benjamin Haibe-Kains ·

Predicting outcomes, such as survival or metastasis for individual cancer patients is a crucial component of precision oncology. Machine learning (ML) offers a promising way to exploit rich multi-modal data, including clinical information and imaging to learn predictors of disease trajectory and help inform clinical decision making. In this paper, we present a novel graph-based approach to incorporate imaging characteristics of existing cancer spread to local lymph nodes (LNs) as well as their connectivity patterns in a prognostic ML model. We trained an edge-gated Graph Convolutional Network (Gated-GCN) to accurately predict the risk of distant metastasis (DM) by propagating information across the LN graph with the aid of soft edge attention mechanism. In a cohort of 1570 head and neck cancer patients, the Gated-GCN achieves AUROC of 0.757 for 2-year DM classification and $C$-index of 0.725 for lifetime DM risk prediction, outperforming current prognostic factors as well as previous approaches based on aggregated LN features. We also explored the importance of graph structure and individual lymph nodes through ablation experiments and interpretability studies, highlighting the importance of considering individual LN characteristics as well as the relationships between regions of cancer spread.

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