# Automatic Report Generation for Histopathology images using pre-trained Vision Transformers and BERT

arXiv: https://arxiv.org/abs/2312.01435 · HTML: https://mlsanity.com/paper/2312.01435/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 15 of its 31 references that are in the map.
- First posted on arXiv 3 Dec 2023.

## Builds on (most cited first, 15 of 15)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Show, Attend and Tell: Neural Image Caption Generation with Visual Attention](https://mlsanity.com/paper/1502.03044/) (2015)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [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)
- [TrOCR: Transformer-based Optical Character Recognition with Pre-trained Models](https://mlsanity.com/paper/2109.10282/) (2021)
- [Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images](https://mlsanity.com/paper/2306.07831/) (2023)
- [Multiple Instance Captioning: Learning Representations from Histopathology Textbooks and Articles](https://mlsanity.com/paper/2103.05121/) (2021)
- [Inference of captions from histopathological patches](https://mlsanity.com/paper/2202.03432/) (2022)
- [Is Attention Interpretation? A Quantitative Assessment On Sets](https://mlsanity.com/paper/2207.13018/) (2022)
- [An Eye on Clinical BERT: Investigating Language Model Generalization for Diabetic Eye Disease Phenotyping](https://mlsanity.com/paper/2311.08687/) (2023)

## Abstract (arXiv)

Deep learning for histopathology has been successfully used for disease classification, image segmentation and more. However, combining image and text modalities using current state-of-the-art (SOTA) methods has been a challenge due to the high resolution of histopathology images. Automatic report generation for histopathology images is one such challenge. In this work, we show that using an existing pre-trained Vision Transformer (ViT) to encode 4096x4096 sized patches of the Whole Slide Image (WSI) and a pre-trained Bidirectional Encoder Representations from Transformers (BERT) model for language modeling-based decoder for report generation, we can build a performant and portable report generation mechanism that takes into account the whole high resolution image. Our method allows us to not only generate and evaluate captions that describe the image, but also helps us classify the image into tissue types and the gender of the patient as well. Our best performing model achieves a 89.52% accuracy in Tissue Type classification with a BLEU-4 score of 0.12 in our caption generation task.