# GRAPHITE: Graph-Based Interpretable Tissue Examination for Enhanced Explainability in Breast Cancer Histopathology

arXiv: https://arxiv.org/abs/2501.04206 · HTML: https://mlsanity.com/paper/2501.04206/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 16 of its 82 references that are in the map.
- First posted on arXiv 8 Jan 2025.

## Builds on (most cited first, 16 of 16)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization](https://mlsanity.com/paper/1610.02391/) (2016)
- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- ["Why Should I Trust You?": Explaining the Predictions of Any Classifier](https://mlsanity.com/paper/1602.04938/) (2016)
- [Learning Important Features Through Propagating Activation Differences](https://mlsanity.com/paper/1704.02685/) (2017)
- [Grad-CAM++: Improved Visual Explanations for Deep Convolutional Networks](https://mlsanity.com/paper/1710.11063/) (2017)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [Cross-Entropy Loss Functions: Theoretical Analysis and Applications](https://mlsanity.com/paper/2304.07288/) (2023)
- [Full-Gradient Representation for Neural Network Visualization](https://mlsanity.com/paper/1905.00780/) (2019)
- [Eigen-CAM: Class Activation Map using Principal Components](https://mlsanity.com/paper/2008.00299/) (2020)
- [Explainable artificial intelligence (XAI) in deep learning-based medical image analysis](https://mlsanity.com/paper/2107.10912/) (2021)
- [Learn To Pay Attention](https://mlsanity.com/paper/1804.02391/) (2018)
- [Distribution-aware Margin Calibration for Semantic Segmentation in Images](https://mlsanity.com/paper/2112.11554/) (2021)

## Built on by (most cited first, 1 of 1)

- [Explainable Artificial Intelligence (XAI) in Computational Pathology: Definitions, Taxonomy, and Recommendations](https://mlsanity.com/paper/2608.28820/) (2026)

## Abstract (arXiv)

Explainable AI (XAI) in medical histopathology is essential for enhancing the interpretability and clinical trustworthiness of deep learning models in cancer diagnosis. However, the black-box nature of these models often limits their clinical adoption. We introduce GRAPHITE (Graph-based Interpretable Tissue Examination), a post-hoc explainable framework designed for breast cancer tissue microarray (TMA) analysis. GRAPHITE employs a multiscale approach, extracting patches at various magnification levels, constructing an hierarchical graph, and utilising graph attention networks (GAT) with scalewise attention (SAN) to capture scale-dependent features. We trained the model on 140 tumour TMA cores and four benign whole slide images from which 140 benign samples were created, and tested it on 53 pathologist-annotated TMA samples. GRAPHITE outperformed traditional XAI methods, achieving a mean average precision (mAP) of 0.56, an area under the receiver operating characteristic curve (AUROC) of 0.94, and a threshold robustness (ThR) of 0.70, indicating that the model maintains high performance across a wide range of thresholds. In clinical utility, GRAPHITE achieved the highest area under the decision curve (AUDC) of 4.17e+5, indicating reliable decision support across thresholds. These results highlight GRAPHITE's potential as a clinically valuable tool in computational pathology, providing interpretable visualisations that align with the pathologists' diagnostic reasoning and support precision medicine.