| --- |
| pretty_name: PRIMO blind benchmark inputs |
| license: other |
| --- |
| |
| # PRIMO public inputs |
|
|
| Blind expression inputs for the PRIMO patient-representation benchmark. |
| `datasets.yaml` lists opaque ids, modalities, paths, and dimensions; clinical |
| targets, provenance, donor ids, and cohort metadata remain private. |
|
|
| Each `<dataset_id>/expression.h5ad` stores raw counts in `X`, NCBI Gene IDs in |
| `var_names`, and symbols in `var["gene_symbols"]`. |
|
|
| - Bulk RNA files have samples as rows and opaque sample ids in `obs_names`. |
| - Single-cell RNA files are sparse and have cells as rows. Cell ids in |
| `obs_names` are opaque. Their only `obs` column is `sample_id`, an opaque |
| collection-sample id shared by cells from the same prediction unit. |
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|
| Each submission covers one selected modality. Submissions are sample-level: |
| produce one embedding per unique `obs["sample_id"]`, with repeated collection |
| timepoints kept separate. |
|
|
| The standalone quickstart in the |
| [PRIMO evaluator Space](https://huggingface.co/spaces/PRIMOmics/primo-eval/blob/main/quickstart.py) |
| shows the modality-specific download and submission flow. Its single-cell example |
| applies per-cell |
| `log2(CP10K + 1)`, mean-pools by `sample_id`, then runs sample-level PCA. |
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|
