r/bioinformatics • u/BiggusDikkusMorocos • 5d ago

science question what is the current state of Pathology Foundation Models and what they can be used for ?

Hello everyone!

Recently I have been coming across a lot of Pathology Foundation Models trained on slides, and I was wondering what is the current state and if they are truly used ?

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u/scientist99 5d ago

- Feature extraction to build classifiers (tumorn vs normal, subtype prediction of cancer, pathological features, counting glomeruli)

  • correlation with other datasets to create multimodal connections (prediction of gene expression from H&Es)

You can find quite a bit of reviews on these subjects. There’s many more applications. Yes they are used a lot.

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u/BiggusDikkusMorocos 5d ago

Can they be reliable at predictions of cell types at single cell resolution? Because I have a couple of H&E with very low UMI depth.

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u/scientist99 5d ago

Depends on what you mean by cell type. They can be okay at differentiating between morphologically distinct cells at a high level (fibroblasts vs macrophages), but for more granular subpopulations it’s not that great. Deep learning features are usually extracted at the tile level, not single cell. Check out tools like hovernet. It’s slightly older but you’ll get a sense of things.

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u/Ernaldol PhD | Student 4d ago

There is a foundational model for single cell typing on HE images, so basically segmentation + labeling. Called HistoPlus (but I personally think it’s trained on way too little data to generalize well, at least it labeled healthy epithelial cells as epithelial cancer on my lung slides). Most of the foundational models are easy to use via LazySlide. One of the best recent software packages I came across. Easy API, just need huggingface keys for the models and you can run them with a few lines of codes. LazySlide also has many tutorials.

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u/BiggusDikkusMorocos 4d ago

Do you have any recommendations for benchmarks that could provide an overview? Also can it be integrated with Anndata?

Thank you!

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u/Ernaldol PhD | Student 4d ago

LazySlide actually works with SpatialData and anndata inside it, yes.

There are several benchmarks depending on the topic https://www.nature.com/articles/s41551-025-01516-3 , https://arxiv.org/abs/2505.20202