# Cross-Modal Knowledge Distillation from Spatial Transcriptomics to Histology

arXiv: https://arxiv.org/abs/2604.09076 · HTML: https://mlsanity.com/paper/2604.09076/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 28 references that are in the map.
- First posted on arXiv 10 Apr 2026.

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

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [FitNets: Hints for Thin Deep Nets](https://mlsanity.com/paper/1412.6550/) (2014)
- [Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning](https://mlsanity.com/paper/2306.01859/) (2023)
- [Transcriptomics-guided Slide Representation Learning in Computational Pathology](https://mlsanity.com/paper/2405.11618/) (2024)
- [A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics](https://mlsanity.com/paper/2508.01490/) (2025)

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

- [BioKERN: Biological Kernel Regularization for Histology-to-Transcriptomics Neighborhood Retrieval](https://mlsanity.com/paper/2608.24823/) (2026)

## Abstract (arXiv)

Spatial transcriptomics provides a molecularly rich description of tissue organization, enabling unsupervised discovery of tissue niches -- spatially coherent regions of distinct cell-type composition and function that are relevant to both biological research and clinical interpretation. However, spatial transcriptomics remains costly and scarce, while H&E histology is abundant but carries a less granular signal. We propose to leverage paired spatial transcriptomics and H&E data to transfer transcriptomics-derived niche structure to a histology-only model via cross-modal distillation. Across multiple tissue types and disease contexts, the distilled model achieves substantially higher agreement with transcriptomics-derived niche structure than unsupervised morphology-based baselines trained on identical image features, and recovers biologically meaningful neighborhood composition as confirmed by cell-type analysis. The resulting framework leverages paired spatial transcriptomic and H&E data during training, and can then be applied to held-out tissue regions using histology alone, without any transcriptomic input at inference time.