Add validated gene-expression checkpoints
Browse filesAdds 12-fold K562 and GM12878 RNA/CAGE EPInformer-v2 f3 checkpoint sets with pooled evaluation metrics.
- expression_models/GM12878/CAGE/fold_10_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_11_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_12_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_1_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_2_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_3_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_4_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_5_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_6_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_7_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_8_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/CAGE/fold_9_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_10_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_11_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_12_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_1_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_2_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_3_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_4_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_5_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_6_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_7_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_8_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/GM12878/RNA/fold_9_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_10_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_11_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_12_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_1_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_2_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_3_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_4_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_5_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_6_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_7_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_8_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/CAGE/fold_9_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_10_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_11_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_12_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_1_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_2_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_3_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_4_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_5_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_6_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_7_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_8_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/K562/RNA/fold_9_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt +3 -0
- expression_models/README.md +21 -0
expression_models/GM12878/CAGE/fold_10_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_11_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_12_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_1_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_2_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_3_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_4_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_5_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_6_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_7_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/CAGE/fold_8_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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version https://git-lfs.github.com/spec/v1
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expression_models/GM12878/CAGE/fold_9_best_EPInformerV2.preTrainedConv.GM12878.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/RNA/fold_10_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/RNA/fold_11_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/RNA/fold_12_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/GM12878/RNA/fold_1_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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version https://git-lfs.github.com/spec/v1
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expression_models/GM12878/RNA/fold_2_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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version https://git-lfs.github.com/spec/v1
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expression_models/GM12878/RNA/fold_3_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:076642fc2db545400ce614748c61427561f7dfff03d6b977a2f483ad53166d9b
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expression_models/GM12878/RNA/fold_4_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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version https://git-lfs.github.com/spec/v1
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expression_models/GM12878/RNA/fold_5_best_EPInformerV2.preTrainedConv.GM12878.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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version https://git-lfs.github.com/spec/v1
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ADDED
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expression_models/K562/CAGE/fold_5_best_EPInformerV2.preTrainedConv.K562.CAGE.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
ADDED
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ADDED
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expression_models/K562/RNA/fold_10_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/K562/RNA/fold_5_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/K562/RNA/fold_8_best_EPInformerV2.preTrainedConv.K562.RNA.60enhs.3feats.rnafeats.prmsig.nonrmprmseq.100kb2TSS_checkpoint.pt
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expression_models/README.md
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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).
|