# Fluoroformer: Scaling multiple instance learning to multiplexed images via attention-based channel fusion

arXiv: https://arxiv.org/abs/2411.08975 · HTML: https://mlsanity.com/paper/2411.08975/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 6 of its 40 references that are in the map.
- First posted on arXiv 13 Nov 2024.

## Builds on (most cited first, 6 of 6)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [Decoupled Weight Decay Regularization](https://mlsanity.com/paper/1711.05101/) (2017)

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

- [AdvDINO: Domain-Adversarial Self-Supervised Representation Learning for Spatial Proteomics](https://mlsanity.com/paper/2508.04955/) (2025)

## Abstract (arXiv)

Though multiple instance learning (MIL) has been a foundational strategy in computational pathology for processing whole slide images (WSIs), current approaches are designed for traditional hematoxylin and eosin (H&E) slides rather than emerging multiplexed technologies. Here, we present an MIL strategy, the Fluoroformer module, that is specifically tailored to multiplexed WSIs by leveraging scaled dot-product attention (SDPA) to interpretably fuse information across disparate channels. On a cohort of 434 non-small cell lung cancer (NSCLC) samples, we show that the Fluoroformer both obtains strong prognostic performance and recapitulates immuno-oncological hallmarks of NSCLC. Our technique thereby provides a path for adapting state-of-the-art AI techniques to emerging spatial biology assays.