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 |