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virtual-spatial-transcriptomics

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ratschlab / uncertainty-vst-2026

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Code for "Probabilistic uncertainty in virtual spatial transcriptomics from histology is largely redundant with the predicted mean" (bioRxiv 2026). Benchmark of aleatoric and epistemic uncertainty (Gaussian/Poisson/NB heads, deep ensembles, MC dropout, Laplace) for gene expression predicted from H&E on 10x Visium.

benchmark bioinformatics snakemake deep-learning pytorch calibration uncertainty-quantification uncertainty-estimation histology digital-pathology bayesian-deep-learning computational-pathology mc-dropout spatial-transcriptomics laplace-approximation histopathology visium gene-expression-prediction deep-ensembles virtual-spatial-transcriptomics
  • Updated Oct 24, 2026
  • Jupyter Notebook

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