# Language models are good pathologists: using attention-based sequence reduction and text-pretrained transformers for efficient WSI classification

arXiv: https://arxiv.org/abs/2211.07384 · HTML: https://mlsanity.com/paper/2211.07384/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 55 of its 79 references that are in the map.
- First posted on arXiv 14 Nov 2022.

## Builds on (most cited first, 30 of 55)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Training Verifiers to Solve Math Word Problems](https://mlsanity.com/paper/2110.14168/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Photorealistic Text-to-Image Diffusion Models with Deep Language Understanding](https://mlsanity.com/paper/2205.11487/) (2022)
- [Zero-Shot Text-to-Image Generation](https://mlsanity.com/paper/2102.12092/) (2021)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [XLNet: Generalized Autoregressive Pretraining for Language Understanding](https://mlsanity.com/paper/1906.08237/) (2019)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Quantization and Training of Neural Networks for Efficient Integer-Arithmetic-Only Inference](https://mlsanity.com/paper/1712.05877/) (2017)
- [fairseq: A Fast, Extensible Toolkit for Sequence Modeling](https://mlsanity.com/paper/1904.01038/) (2019)
- [Linformer: Self-Attention with Linear Complexity](https://mlsanity.com/paper/2006.04768/) (2020)
- [Rethinking Semantic Segmentation from a Sequence-to-Sequence Perspective with Transformers](https://mlsanity.com/paper/2012.15840/) (2020)
- [Mixed Precision Training](https://mlsanity.com/paper/1710.03740/) (2017)
- [EfficientNetV2: Smaller Models and Faster Training](https://mlsanity.com/paper/2104.00298/) (2021)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Aligning Books and Movies: Towards Story-like Visual Explanations by Watching Movies and Reading Books](https://mlsanity.com/paper/1506.06724/) (2015)
- [Language Models as Zero-Shot Planners: Extracting Actionable Knowledge for Embodied Agents](https://mlsanity.com/paper/2201.07207/) (2022)
- [What Does BERT Look At? An Analysis of BERT's Attention](https://mlsanity.com/paper/1906.04341/) (2019)
- [Scaling Vision Transformers](https://mlsanity.com/paper/2106.04560/) (2021)
- [Training Deep Nets with Sublinear Memory Cost](https://mlsanity.com/paper/1604.06174/) (2016)
- [A Primer in BERTology: What we know about how BERT works](https://mlsanity.com/paper/2002.12327/) (2020)
- [Quantifying Attention Flow in Transformers](https://mlsanity.com/paper/2005.00928/) (2020)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)

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

- [PathoDuet: Foundation Models for Pathological Slide Analysis of H&E and IHC Stains](https://mlsanity.com/paper/2312.09894/) (2023)

## Abstract (arXiv)

In digital pathology, Whole Slide Image (WSI) analysis is usually formulated as a Multiple Instance Learning (MIL) problem. Although transformer-based architectures have been used for WSI classification, these methods require modifications to adapt them to specific challenges of this type of image data. Among these challenges is the amount of memory and compute required by deep transformer models to process long inputs, such as the thousands of image patches that can compose a WSI at × 10 or × 20 magnification. We introduce textitSeqShort, a multi-head attention-based sequence shortening layer to summarize each WSI in a fixed- and short-sized sequence of instances, that allows us to reduce the computational costs of self-attention on long sequences, and to include positional information that is unavailable in other MIL approaches. Furthermore, we show that WSI classification performance can be improved when the downstream transformer architecture has been pre-trained on a large corpus of text data, and only fine-tuning less than 0.1% of its parameters. We demonstrate the effectiveness of our method in lymph node metastases classification and cancer subtype classification tasks, without the need of designing a WSI-specific transformer nor doing in-domain pre-training, keeping a reduced compute budget and low number of trainable parameters.