# MINT: Molecularly Informed Training with Spatial Transcriptomics Supervision for Pathology Foundation Models

arXiv: https://arxiv.org/abs/2603.07895 · HTML: https://mlsanity.com/paper/2603.07895/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 10 of its 26 references that are in the map.
- First posted on arXiv 9 Mar 2026.

## Builds on (most cited first, 10 of 10)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology](https://mlsanity.com/paper/2408.00738/) (2024)
- [HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis](https://mlsanity.com/paper/2406.16192/) (2024)
- [Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning](https://mlsanity.com/paper/2306.01859/) (2023)
- [Phikon-v2, A large and public feature extractor for biomarker prediction](https://mlsanity.com/paper/2409.09173/) (2024)
- [Hibou: A Family of Foundational Vision Transformers for Pathology](https://mlsanity.com/paper/2406.05074/) (2024)
- [Distilling foundation models for robust and efficient models in digital pathology](https://mlsanity.com/paper/2501.16239/) (2025)
- [Training state-of-the-art pathology foundation models with orders of magnitude less data](https://mlsanity.com/paper/2504.05186/) (2025)

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

- [Bridging the Modality Bottleneck in Pathology MIL through Virtual Molecular Staining](https://mlsanity.com/paper/2605.16392/) (2026)

## Abstract (arXiv)

Pathology foundation models learn morphological representations through self-supervised pretraining on large-scale whole-slide images, yet they do not explicitly capture the underlying molecular state of the tissue. Spatial transcriptomics technologies bridge this gap by measuring gene expression in situ, offering a natural cross-modal supervisory signal. We propose MINT (Molecularly Informed Training), a fine-tuning framework that incorporates spatial transcriptomics supervision into pretrained pathology Vision Transformers. MINT appends a learnable ST token to the ViT input to encode transcriptomic information separately from the morphological CLS token, preventing catastrophic forgetting through DINO self-distillation and explicit feature anchoring to the frozen pretrained encoder. Gene expression regression at both spot-level (Visium) and patch-level (Xenium) resolutions provides complementary supervision across spatial scales. Trained on 577 publicly available HEST samples, MINT achieves the best overall performance on both HEST-Bench for gene expression prediction (mean Pearson r = 0.440) and EVA for general pathology tasks (0.803), demonstrating that spatial transcriptomics supervision complements morphology-centric self-supervised pretraining.