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ProtoGTX: Prototype-Aligned Graph Transformer for Explainable Whole-Slide Image Analysis

Iori Azuma, Hiroyuki Kusuhara, Tadahaya Mizuno · 2026 · arXiv (Cornell University)

DOI: 10.48550/arxiv.2610.24023 · cited by 0 works (OpenAlex) · open-access PDF

French

L'apprentissage profond a atteint de fortes performances en pathologie computaire, mais l'explication des prédictions d'image de diapositive (WSI) reste difficile. Les méthodes d'explication existantes mettent souvent en évidence des régions importantes sans identifier leurs modèles morphologiques, laissant un fossé entre les preuves computables au niveau des patchs et l'interprétation pathologique au niveau des diapositives. Nous proposons ProtoGTX, un cadre basé sur des graphiques qui combine la contextualisation spatiale avec un vocabulaire de prototype morphologique flexible. ProtoGTX sépare les prototypes de référence utilisés pour définir les concepts morphologiques du modèle prédictif: le vocabulaire de référence sur l'interpr

Machine translation (Meta M2M100); the English original follows.

Abstract

Deep learning has achieved strong performance in computational pathology, but explaining whole-slide image (WSI) predictions remains challenging. Existing explanation methods often highlight important regions without identifying their morphological patterns, leaving a gap between patch-level computational evidence and slide-level pathological interpretation. We propose ProtoGTX, a graph-based framework that combines spatial contextualization with a flexible morphological prototype vocabulary. ProtoGTX separates the reference prototypes used to define morphological concepts from the predictive model: the reference vocabulary can be generated from training data by unsupervised clustering or supplied externally, and remains fixed during classifier training. Patch features are first contextualized over a spatial graph, after which learnable prototypes representing morphological concepts are optimized through cross-attention. Their slide-level activation profile is aligned with the morphological composition induced by the fixed reference prototype bank. On the CPTAC and BRACS datasets, ProtoGTX outperforms the evaluated MIL, prototype-based, and graph-based baselines, with particularly pronounced improvements on BRACS. Qualitative analyses further show that spatial contextualization transforms fragmented patch-level prototype assignments into more coherent tissue regions. In BRACS, prototype maps also co-localize with pathologist annotations and regions relevant to slide-level prediction. These results demonstrate that ProtoGTX provides complementary semantic and spatial explanations while retaining a prototype vocabulary that can be defined independently of the predictive model. Code is available at https://github.com/mizuno-group/ProtoGTX.

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Topics: Computer science, Vocabulary, Artificial intelligence, Contextualization, Classifier (UML), Cluster analysis

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