# On the calibration of neural networks for histological slide-level classification

arXiv: https://arxiv.org/abs/2312.09719 · HTML: https://mlsanity.com/paper/2312.09719/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 27 references that are in the map.
- First posted on arXiv 15 Dec 2023.

## Builds on (most cited first, 14 of 14)

- [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)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [Can You Trust Your Model's Uncertainty? Evaluating Predictive Uncertainty Under Dataset Shift](https://mlsanity.com/paper/1906.02530/) (2019)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Revisiting the Calibration of Modern Neural Networks](https://mlsanity.com/paper/2106.07998/) (2021)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [Self supervised contrastive learning for digital histopathology](https://mlsanity.com/paper/2011.13971/) (2020)
- [A Generalized Deep Learning Framework for Whole-Slide Image Segmentation and Analysis](https://mlsanity.com/paper/2001.00258/) (2020)
- [A Survey on Graph-Based Deep Learning for Computational Histopathology](https://mlsanity.com/paper/2107.00272/) (2021)
- [Benchmarking common uncertainty estimation methods with histopathological images under domain shift and label noise](https://mlsanity.com/paper/2301.01054/) (2023)
- [Predicting microsatellite instability and key biomarkers in colorectal cancer from H&E-stained images: Achieving SOTA predictive performance with fewer data using Swin Transformer](https://mlsanity.com/paper/2208.10495/) (2022)

## Abstract (arXiv)

Deep Neural Networks have shown promising classification performance when predicting certain biomarkers from Whole Slide Images in digital pathology. However, the calibration of the networks' output probabilities is often not evaluated. Communicating uncertainty by providing reliable confidence scores is of high relevance in the medical context. In this work, we compare three neural network architectures that combine feature representations on patch-level to a slide-level prediction with respect to their classification performance and evaluate their calibration. As slide-level classification task, we choose the prediction of Microsatellite Instability from Colorectal Cancer tissue sections. We observe that Transformers lead to good results in terms of classification performance and calibration. When evaluating the classification performance on a separate dataset, we observe that Transformers generalize best. The investigation of reliability diagrams provides additional insights to the Expected Calibration Error metric and we observe that especially Transformers push the output probabilities to extreme values, which results in overconfident predictions.