# FEAST: Fully Connected Expressive Attention for Spatial Transcriptomics

arXiv: https://arxiv.org/abs/2603.25247 · HTML: https://mlsanity.com/paper/2603.25247/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 35 references that are in the map.
- First posted on arXiv 26 Mar 2026.

## Builds on (most cited first, 7 of 7)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation](https://mlsanity.com/paper/2108.12409/) (2021)
- [Multimodal Whole Slide Foundation Model for Pathology](https://mlsanity.com/paper/2411.19666/) (2024)
- [Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning](https://mlsanity.com/paper/2306.01859/) (2023)
- [Accurate Spatial Gene Expression Prediction by integrating Multi-resolution features](https://mlsanity.com/paper/2403.07592/) (2024)
- [MERGE: Multi-faceted Hierarchical Graph-based GNN for Gene Expression Prediction from Whole Slide Histopathology Images](https://mlsanity.com/paper/2412.02601/) (2024)
- [Spatially Gene Expression Prediction using Dual-Scale Contrastive Learning](https://mlsanity.com/paper/2506.23827/) (2025)

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

- [Contrastive and Adaptive Multi-modal Masked Autoencoder for Spatial Transcriptomics](https://mlsanity.com/paper/2606.21156/) (2026)

## Abstract (arXiv)

Spatial Transcriptomics (ST) provides spatially-resolved gene expression, offering crucial insights into tissue architecture and complex diseases. However, its prohibitive cost limits widespread adoption, leading to significant attention on inferring spatial gene expression from readily available whole slide images. While graph neural networks have been proposed to model interactions between tissue regions, their reliance on pre-defined sparse graphs prevents them from considering potentially interacting spot pairs, resulting in a structural limitation in capturing complex biological relationships. To address this, we propose FEAST (Fully connected Expressive Attention for Spatial Transcriptomics), an attention-based framework that models the tissue as a fully connected graph, enabling the consideration of all pairwise interactions. To better reflect biological interactions, we introduce negative-aware attention, which models both excitatory and inhibitory interactions, capturing essential negative relationships that standard attention often overlooks. Furthermore, to mitigate the information loss from truncated or ignored context in standard spot image extraction, we introduce an off-grid sampling strategy that gathers additional images from intermediate regions, allowing the model to capture a richer morphological context. Experiments on public ST datasets show that FEAST surpasses state-of-the-art methods in gene expression prediction while providing biologically plausible attention maps that clarify positive and negative interactions. Our code is available at https://github.com/starforTJ/ FEAST.