Relational Graph Convolutional Network for Robust Mass Spectrum Classification

Supervised machine learning methods have shown impressive performance in interpreting mass signals and automatically segmenting spatially meaningful regions in Mass Spectrometry Imaging (MSI). Such segmentation generates maps that provide researchers with valuable insights into sample composition and serve as a foundation for downstream statistical analyses. However, these models often require data set-specific preprocessing and do not fully exploit the rich mass features available in high-resolution mass spectrometry (HRMS). Unlike low-resolution mass spectrometry, HRMS reveals additional features such as mass defects and repeated mass differences that carry important chemical information. In this work, we propose a novel deep learning architecture based on a Relational Graph Convolutional Network (R-GCN) that captures and leverages those HRMS mass features. Our model explicitly encodes structural features such as mass defects and known mass differences to represent each spectrum as a graph, enabling the learning of associations between chemically related ion families. To the best of our knowledge, no existing deep learning models for MSI classification incorporate this level of chemically informed mass structure. Most existing methods treat spectra as flat vectors or image-like inputs, thereby ignoring the underlying mass relationships. We evaluate our R-GCN approach against several conventional machine learning and deep learning baselines across diverse MSI data sets, demonstrating its robustness to common signal variations (e.g., mass shift, ion loss). Finally, we integrate Class Activation Mapping (CAM) to enhance model interpretability, enabling the identification of ion families that are relevant to specific biological or spatial regions.