# scripts/common

system-agnostic training + eval + inference. everything here takes a system name
(`pan_skin`, `hematopoiesis`, `pancreas`) as an argument and expects the corresponding
`data/corpus/{system}/harmonized/corpus.h5ad`.

| script | what it does |
|---|---|
| `train_panda.py` | train one PANDA variant (pca / marker) on one system |
| `cv_holdout.py`  | 5-fold held-out CV (GroupKFold by dataset when available) |
| `zero_shot.py`   | run PANDA checkpoints on Dingwall / Dahlin / Veres targets |
| `nestorowa_zero_shot.py` | labeled zero-shot on Nestorowa GSE81682 (HSC validation) |
| `extract_prototypes_for_analysis.py` | prototype extraction helper for downstream analysis scripts |
| `rerun_all_discovery.sh` | driver that re-runs the whole `scripts/analysis/` block end to end |