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arXiv · 2502.05458

Block Graph Neural Networks for tumor heterogeneity prediction

Marianne Abémgnigni Njifon·Tobias Weber·Viktor Bezborodov·Tyll Krueger·Dominic Schuhmacher
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Abstract

Accurate tumor classification is essential for selecting effective treatments, but current methods have limitations. Standard tumor grading, which categorizes tumors based on cell differentiation, is not recommended as a stand-alone procedure, as some well-differentiated tumors can be malignant. Tumor heterogeneity assessment via single-cell sequencing offers profound insights but can be costly and may still require significant manual intervention. Many existing statistical machine learning methods for tumor data still require complex pre-processing of MRI and histopathological data. In this paper, we propose to build on a mathematical model that simulates tumor evolution (Ożański (2017)) and generate artificial datasets for tumor classification. Tumor heterogeneity is estimated using normalized entropy, with a threshold to classify tumors as having high or low heterogeneity. Our contributions are threefold: (1) the cut and graph generation processes from the artificial data, (2) the design of tumor features, and (3) the construction of Block Graph Neural Networks (BGNN), a Graph Neural Network-based approach to predict tumor heterogeneity. The experimental results reveal that the combination of the proposed features and models yields excellent results on artificially generated data ($89.67\%$ accuracy on the test data). In particular, in alignment with the emerging trends in AI-assisted grading and spatial transcriptomics, our results suggest that enriching traditional grading methods with birth (e.g., Ki-67 proliferation index) and death markers can improve heterogeneity prediction and enhance tumor classification.

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Marianne Abémgnigni Njifon, Tobias Weber, Viktor Bezborodov, Tyll Krueger, Dominic Schuhmacher. 2025-02-08. Block Graph Neural Networks for tumor heterogeneity prediction. https://arxiv.org/abs/2502.05458

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