Document expression checkpoint layout

README.md

@@ -40,12 +40,18 @@ CAGE labels exist only for K562/GM12878 (the other four are RNA-only).
 
 ```
 enhancer_encoders/{CELL}/fold_{i}.pt   # CELL ∈ {K562, GM12878, H1, HepG2, HUVEC, NHEK}, i ∈ 1..12
+expression_models/{CELL}/{ASSAY}/{FEATURE}/fold_*.pt
+# ASSAY ∈ {RNA, CAGE}; FEATURE ∈ {f1, f2, f3}
 ```
 
 These are the pipeline's **256 bp enhancer-activity encoders** — the best checkpoint for each of
 the 12 leave-chromosome-out folds, for all 6 cell lines (72 checkpoints). Any fold works for
 inference; the R values in the table above are pooled across all 12 held-out folds.
 
+The gene-expression checkpoint directories contain 12 folds for each supported cell/assay/feature
+configuration. Use the matching HDF5 input, expression labels, fold split, and pretrained enhancer
+encoder described in the pipeline README.
+
 > The KLF1 demo in the notebooks uses the original published EPInformer encoder shipped in the repo's
 > `trained_models/pretrained_enhancer_encoder/` — a separate checkpoint from these folds.