Archive 4 checkpoints (1-4)

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+group,metric,question,compared_against,reference
+Cells,Precision / coverage,Land on real cells? Cover all real cells?,held-out real cells (R2),Kynkäänniemi 2019; Naeem 2020
+Cells,Classifier AUC,Can a classifier tell generated from real cells?,0.5 = indistinguishable,Lopez-Paz & Oquab 2017
+Cells,MMD²,How far apart are the two cell distributions?,real vs real,Gretton 2012
+Cells,E_N,scSemiProfiler's own nearest-neighbour error,within-sample split,Wang 2024
+Composition,Cell-type L1,Right mix of the six scANVI cell types?,other donors' mean (null),—
+Disease,logFC r (Pearson / Spearman),Same case-vs-control change in each cell type?,broadcast; split-half ceiling,Roohani 2024; Viñas Torné 2026
+Disease,Top-50 DEG overlap,Same top disease genes per cell type?,chance; limma-voom check,Li 2026; Squair 2021; Law 2014
+Disease,CAT curve,Same genes at every list length k?,chance = k / 2G,Irizarry 2005
+Cost,GPU time,How long to apply to a new cohort?,"same donors, same GPU",—