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JiecongLin
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EPInformer

PyTorch
biology
genomics
gene-expression
enhancer
regulatory-genomics
dna
Model card Files
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JiecongLin commited on
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Add all 6 enhancer encoders (12 leave-chromosome-out folds each) + update model card

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  1. README.md +7 -2
  2. enhancer_encoders/GM12878/fold_1.pt +3 -0
  3. enhancer_encoders/GM12878/fold_10.pt +3 -0
  4. enhancer_encoders/GM12878/fold_11.pt +3 -0
  5. enhancer_encoders/GM12878/fold_12.pt +3 -0
  6. enhancer_encoders/GM12878/fold_2.pt +3 -0
  7. enhancer_encoders/GM12878/fold_3.pt +3 -0
  8. enhancer_encoders/GM12878/fold_4.pt +3 -0
  9. enhancer_encoders/GM12878/fold_5.pt +3 -0
  10. enhancer_encoders/GM12878/fold_6.pt +3 -0
  11. enhancer_encoders/GM12878/fold_7.pt +3 -0
  12. enhancer_encoders/GM12878/fold_8.pt +3 -0
  13. enhancer_encoders/GM12878/fold_9.pt +3 -0
  14. enhancer_encoders/H1/fold_1.pt +3 -0
  15. enhancer_encoders/H1/fold_10.pt +3 -0
  16. enhancer_encoders/H1/fold_11.pt +3 -0
  17. enhancer_encoders/H1/fold_12.pt +3 -0
  18. enhancer_encoders/H1/fold_2.pt +3 -0
  19. enhancer_encoders/H1/fold_3.pt +3 -0
  20. enhancer_encoders/H1/fold_4.pt +3 -0
  21. enhancer_encoders/H1/fold_5.pt +3 -0
  22. enhancer_encoders/H1/fold_6.pt +3 -0
  23. enhancer_encoders/H1/fold_7.pt +3 -0
  24. enhancer_encoders/H1/fold_8.pt +3 -0
  25. enhancer_encoders/H1/fold_9.pt +3 -0
  26. enhancer_encoders/HUVEC/fold_1.pt +3 -0
  27. enhancer_encoders/HUVEC/fold_10.pt +3 -0
  28. enhancer_encoders/HUVEC/fold_11.pt +3 -0
  29. enhancer_encoders/HUVEC/fold_12.pt +3 -0
  30. enhancer_encoders/HUVEC/fold_2.pt +3 -0
  31. enhancer_encoders/HUVEC/fold_3.pt +3 -0
  32. enhancer_encoders/HUVEC/fold_4.pt +3 -0
  33. enhancer_encoders/HUVEC/fold_5.pt +3 -0
  34. enhancer_encoders/HUVEC/fold_6.pt +3 -0
  35. enhancer_encoders/HUVEC/fold_7.pt +3 -0
  36. enhancer_encoders/HUVEC/fold_8.pt +3 -0
  37. enhancer_encoders/HUVEC/fold_9.pt +3 -0
  38. enhancer_encoders/HepG2/fold_1.pt +3 -0
  39. enhancer_encoders/HepG2/fold_10.pt +3 -0
  40. enhancer_encoders/HepG2/fold_11.pt +3 -0
  41. enhancer_encoders/HepG2/fold_12.pt +3 -0
  42. enhancer_encoders/HepG2/fold_2.pt +3 -0
  43. enhancer_encoders/HepG2/fold_3.pt +3 -0
  44. enhancer_encoders/HepG2/fold_4.pt +3 -0
  45. enhancer_encoders/HepG2/fold_5.pt +3 -0
  46. enhancer_encoders/HepG2/fold_6.pt +3 -0
  47. enhancer_encoders/HepG2/fold_7.pt +3 -0
  48. enhancer_encoders/HepG2/fold_8.pt +3 -0
  49. enhancer_encoders/HepG2/fold_9.pt +3 -0
  50. enhancer_encoders/K562/fold_1.pt +3 -0
README.md CHANGED
@@ -39,10 +39,15 @@ CAGE labels exist only for K562/GM12878 (the other four are RNA-only).
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  ## Files
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  ```
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- enhancer_encoders/{CELL}/fold_{i}.pt # 256 bp enhancer-activity encoders, 12 leave-chromosome-out folds per cell
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  ```
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- The fold-8 K562 encoder (`enhancer_encoders/K562/fold_8.pt`) is the checkpoint used in the KLF1 enhancer-activity demo notebook.
 
 
 
 
 
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  ## Usage
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  ## Files
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  ```
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+ enhancer_encoders/{CELL}/fold_{i}.pt # CELL ∈ {K562, GM12878, H1, HepG2, HUVEC, NHEK}, i ∈ 1..12
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  ```
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+ These are the reproduction's **256 bp enhancer-activity encoders** — the best checkpoint for each of
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+ the 12 leave-chromosome-out folds, for all 6 cell lines (72 checkpoints). Any fold works for
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+ inference; the R values in the table above are pooled across all 12 held-out folds.
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+
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+ > The KLF1 demo in the notebooks uses the original published EPInformer encoder shipped in the repo's
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+ > `trained_models/pretrained_enhancer_encoder/` — a separate checkpoint from these reproduction folds.
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  ## Usage
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