# MUL-T: Decoding Spatial Cellular Architecture in Multiplexed Tissue Images

arXiv: https://arxiv.org/abs/2607.28030 · HTML: https://mlsanity.com/paper/2607.28030/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 22 references that are in the map.
- First posted on arXiv 30 Jul 2026.

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

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [A Foundation Model for Spatial Proteomics](https://mlsanity.com/paper/2506.03373/) (2025)
- [Mew: Multiplexed Immunofluorescence Image Analysis through an Efficient Multiplex Network](https://mlsanity.com/paper/2407.17857/) (2024)

## Abstract (arXiv)

Understanding tissue organisation in multiplexed imaging requires modelling both cellular phenotypes and their spatial context. Existing approaches typically rely on handcrafted features, such as marker intensity statistics or cell-type proportions, which often fail to scale or generalise across cohorts with heterogeneous marker panels. We introduce MUL-T, a lightweight transformer framework that reframes tissue architecture as a masked contextual prediction task over discrete cell tokens. By learning contextualised [CLS] embeddings without task-specific supervision, the model captures higher-order cellular interactions while remaining computationally efficient. We evaluate MUL-T on several clinically relevant downstream tasks, including core-level tumour pattern classification, patient-level grading, PD-L1 positivity prediction, and cross-dataset treatment response prediction. Across tasks, MUL-T consistently outperforms classical feature-based baselines and achieves performance comparable to a foundation ViT model, despite substantially fewer parameters and lower training cost.