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+. 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, accept its terms, and follow the Pretrained Checkpoints instructions in the GHIST+ README. 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.