WSI-GT: Pseudo-Label Guided Graph Transformer for Whole-Slide Histology

Machine Learning and Knowledge Extraction. 2026. Vol. 8. No. 1. Article 8.

Михайлов И. А.

Whole-slide histology images (WSIs) can exceed 100 k × 100 k pixels, making direct pixel-level segmentation infeasible and requiring patch-level classification as a practical alternative for downstream WSI segmentation. However, most approaches either treat patches independently, ignoring spatial and biological context, or rely on deep graph models prone to oversmoothing and loss of local tissue detail. We present WSI-GT (Pseudo-Label Guided Graph Transformer), a simple yet effective architecture that addresses these challenges and enables accurate WSI-level tissue segmentation. WSI-GT combines a lightweight local graph convolution block for neighborhood feature aggregation with a pseudo-label guided attention mechanism that preserves intra-class variability and mitigates oversmoothing. To cope with sparse annotations, we introduce an area-weighted sampling strategy that balances class representation while maintaining tissue topology. WSI-GT achieves a Macro F1 of 0.95 on PATH-DT-MSU WSS2v2, improving by up to 3 percentage points over patch-based CNNs and by about 2 points over strong graph baselines. It further generalizes well to the Placenta benchmark and standard graph node classification datasets, highlighting both clinical relevance and broader applicability. These results position WSI-GT as a practical and scalable solution for graph-based learning on extremely large images and for generating clinically meaningful WSI segmentations.

Keywords: digital pathology