README.md

---
pretty_name: GHIST+ Data and Model Bundle
license: other
tags:
- spatial-transcriptomics
- computational-pathology
- xenium
---

# GHIST+ data and model bundle

This bundle contains the model artifacts, predictions, evaluation inputs,
comparison outputs, and plot-ready tables released with
[GHIST+](https://github.com/SydneyBioX/GHIST_plus). Source code is provided in
that repository.

## Download

    hf download GHISTPlus/GHIST-Plus-bundle \
      --repo-type dataset \
      --local-dir bundle

The bundle is approximately 38 GB. Individual files can also be downloaded
from this page.

## Model checkpoints

The four released GHIST+ checkpoint files are:

- GHIST_plus/models/breast_multi/ghist_plus_breast_multi_checkpoint.pth
- GHIST_plus/models/breast_single/ghist_plus_breast_single_checkpoint.pth
- GHIST_plus/models/imputation/ghist_plus_gene_imputation_checkpoint.pth
- GHIST_plus/models/pancancer/ghist_plus_pancancer_checkpoint.pth

They exclude the frozen third-party UNI2-H encoder weights. Users must obtain
UNI2-H directly from
[MahmoodLab/UNI2-h](https://huggingface.co/MahmoodLab/UNI2-h), accept its
terms, and follow the **Pretrained Checkpoints** instructions in the
[GHIST+ README](https://github.com/SydneyBioX/GHIST_plus#pretrained-checkpoints).
That procedure reconstructs the complete checkpoints locally at the same
filenames, so the existing inference commands and configs remain unchanged.

The bundle does not redistribute UNI2-H weights.

## Use with the figure notebooks

The simplest layout is:

    download-parent/
    ├── GHIST_plus/
    └── bundle/

Start Jupyter from the code repository root. Figure2.ipynb through
Figure5.ipynb will find ../bundle automatically:

    cd GHIST_plus
    jupyter lab

For another location, set:

    export GHIST_BUNDLE_ROOT="/path/to/bundle"
    jupyter lab

GHIST_BUNDLE_ROOT must point to the bundle directory, not its parent.

## Contents

- **Figure 2:** evaluation data, GHIST+ predictions, and comparison-model
  predictions under evaluation_data/, GHIST_plus/predictions/, and
  other_models/.
- **Figure 3:** imputation inputs and predictions, including the bundled
  VQ/composition ablation predictions.
- **Figure 4:** plot-ready tables under figure_data/figure4/.
- **Figure 5:** paired PCC and coverage tables under figure_data/figure5/.

    bundle/
    ├── GHIST_plus/
    │   ├── models/
    │   └── predictions/
    ├── evaluation_data/
    ├── figure_data/
    └── other_models/

The paths and lightweight input schemas were checked against the released
Figure 2–5 notebooks.

## Data and third-party terms

The bundle combines author-generated artifacts, processed public source data,
and outputs from comparison methods. It therefore has no single blanket
license; the Hugging Face license field is other. See
THIRD_PARTY_NOTICES.md for component-specific sources, versions, attributions,
and terms. Upstream terms remain applicable.

## Tutorial data

tutorial.ipynb does not use this bundle as its DATA_ROOT. The tutorial requires
a separately prepared GHIST data directory containing aligned H&E images,
segmentation masks, nuclei metadata, and inputs for the selected training mode.