JiecongLin commited on
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c517a99
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verified ·
1 Parent(s): b150586

Add validated gene-expression checkpoints

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Adds 12-fold K562 and GM12878 RNA/CAGE EPInformer-v2 f3 checkpoint sets with pooled evaluation metrics.

Files changed (49) hide show
  1. expression_models/GM12878/CAGE/fold_10_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  2. expression_models/GM12878/CAGE/fold_11_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  3. expression_models/GM12878/CAGE/fold_12_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  4. expression_models/GM12878/CAGE/fold_1_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  5. expression_models/GM12878/CAGE/fold_2_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  6. expression_models/GM12878/CAGE/fold_3_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  7. expression_models/GM12878/CAGE/fold_4_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  8. expression_models/GM12878/CAGE/fold_5_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  9. expression_models/GM12878/CAGE/fold_6_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  10. expression_models/GM12878/CAGE/fold_7_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  11. expression_models/GM12878/CAGE/fold_8_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  12. expression_models/GM12878/CAGE/fold_9_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  13. expression_models/GM12878/RNA/fold_10_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  14. expression_models/GM12878/RNA/fold_11_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  15. expression_models/GM12878/RNA/fold_12_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  16. expression_models/GM12878/RNA/fold_1_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  17. expression_models/GM12878/RNA/fold_2_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  18. expression_models/GM12878/RNA/fold_3_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  19. expression_models/GM12878/RNA/fold_4_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  20. expression_models/GM12878/RNA/fold_5_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  21. expression_models/GM12878/RNA/fold_6_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  22. expression_models/GM12878/RNA/fold_7_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  23. expression_models/GM12878/RNA/fold_8_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  24. expression_models/GM12878/RNA/fold_9_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  25. expression_models/K562/CAGE/fold_10_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  26. expression_models/K562/CAGE/fold_11_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  27. expression_models/K562/CAGE/fold_12_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  28. expression_models/K562/CAGE/fold_1_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  29. expression_models/K562/CAGE/fold_2_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  30. expression_models/K562/CAGE/fold_3_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  31. expression_models/K562/CAGE/fold_4_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  32. expression_models/K562/CAGE/fold_5_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  33. expression_models/K562/CAGE/fold_6_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  34. expression_models/K562/CAGE/fold_7_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  35. expression_models/K562/CAGE/fold_8_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  36. expression_models/K562/CAGE/fold_9_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  37. expression_models/K562/RNA/fold_10_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  38. expression_models/K562/RNA/fold_11_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  39. expression_models/K562/RNA/fold_12_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  40. expression_models/K562/RNA/fold_1_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  41. expression_models/K562/RNA/fold_2_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  42. expression_models/K562/RNA/fold_3_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  43. expression_models/K562/RNA/fold_4_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  44. expression_models/K562/RNA/fold_5_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  45. expression_models/K562/RNA/fold_6_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  46. expression_models/K562/RNA/fold_7_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  47. expression_models/K562/RNA/fold_8_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  48. expression_models/K562/RNA/fold_9_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
  49. expression_models/README.md +21 -0
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+ # EPInformer pipeline checkpoints
2
+
3
+ This repository provides the 12-fold leave-chromosome-out checkpoints for the
4
+ EPInformer pipeline.
5
+
6
+ ## Gene-expression checkpoints
7
+
8
+ The `expression_models/` directory contains the validated `f3` models with
9
+ three enhancer features (distance, activity, and Hi-C contact) and promoter
10
+ signal:
11
+
12
+ | Cell type | Assay | Directory | Pooled Pearson R |
13
+ |---|---|---|---:|
14
+ | K562 | RNA | `expression_models/K562/RNA` | 0.8564 |
15
+ | K562 | CAGE | `expression_models/K562/CAGE` | 0.8673 |
16
+ | GM12878 | RNA | `expression_models/GM12878/RNA` | 0.8602 |
17
+ | GM12878 | CAGE | `expression_models/GM12878/CAGE` | 0.8902 |
18
+
19
+ Each directory contains one checkpoint for each fold (1--12). Use the
20
+ matching encoder checkpoints, HDF5 input, expression labels, and fold split
21
+ described in the [EPInformer pipeline README](https://github.com/pinellolab/EPInformer/tree/pipeline).