diff --git a/README.md b/README.md index 2dff1bf4f12b709bfe99ce5b5913bce36e86fad7..77db1926ce333818537e4c0c1c1908106dc9c81b 100644 --- a/README.md +++ b/README.md @@ -39,10 +39,15 @@ CAGE labels exist only for K562/GM12878 (the other four are RNA-only). ## Files ``` -enhancer_encoders/{CELL}/fold_{i}.pt # 256 bp enhancer-activity encoders, 12 leave-chromosome-out folds per cell +enhancer_encoders/{CELL}/fold_{i}.pt # CELL ∈ {K562, GM12878, H1, HepG2, HUVEC, NHEK}, i ∈ 1..12 ``` -The fold-8 K562 encoder (`enhancer_encoders/K562/fold_8.pt`) is the checkpoint used in the KLF1 enhancer-activity demo notebook. +These are the reproduction'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 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 reproduction folds. ## Usage diff --git a/enhancer_encoders/GM12878/fold_1.pt b/enhancer_encoders/GM12878/fold_1.pt new file mode 100644 index 0000000000000000000000000000000000000000..0cef794cec05778e8d9bf432fcf034c12e691ad3 --- /dev/null +++ b/enhancer_encoders/GM12878/fold_1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fe960a3b7267ed64b32391072328928cf50280805f859398b51bf8d301f52ce2 +size 3240225 diff --git a/enhancer_encoders/GM12878/fold_10.pt b/enhancer_encoders/GM12878/fold_10.pt new file mode 100644 index 0000000000000000000000000000000000000000..cd5e3285572a3992e43541556aeef1c0a1b91cdb --- /dev/null +++ b/enhancer_encoders/GM12878/fold_10.pt @@ -0,0 +1,3 @@ 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