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HEST-1k Recipe (Exemplar)

This directory serves as a comprehensive exemplar for training SpatialTranscriptFormer on the HEST-1k benchmark dataset.

While the core SpatialTranscriptFormer framework is dataset-agnostic, this recipe provides a complete, out-of-the-box pipeline for reproducing our benchmarks, including data downloading, preprocessing, and specialized dataloaders.

Components

  • dataset.py: Contains HEST_Dataset and HEST_FeatureDataset, which subclass SpatialDataset to handle the specific .h5ad structure and metadata conventions of the HEST dataset.
  • io.py: Utilities for reading spatial graphs, coordinates, and .h5ad matrices.
  • utils.py: HEST-specific dataset setup routines, splitting logic, and vocabulary loading.
  • download.py: Logic for fetching subsets of the gated HEST dataset from Hugging Face.

Usage

For complete CLI usage and training preset commands, refer to the main README.md and the Training Guide.