Update README.md
Browse files
README.md
CHANGED
|
@@ -1,3 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
# DeepShape
|
| 2 |
|
| 3 |

|
|
@@ -7,3 +45,8 @@ DeepShape is a deep convolutional neural network designed to predict molecular p
|
|
| 7 |
DeepShape is built upon DeeperDeepSEA, a PyTorch-based deep learning model originally designed to predict chromatin features from DNA sequence alone as implemented in [Selene](https://www.nature.com/articles/s41592-019-0360-8).
|
| 8 |
|
| 9 |
https://github.com/ni-lab/DeepShape
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
model-index:
|
| 3 |
+
- name: DeepShape
|
| 4 |
+
results:
|
| 5 |
+
- task:
|
| 6 |
+
name: TF/DNase/Histone Binding Prediction
|
| 7 |
+
type: binary-classification
|
| 8 |
+
dataset:
|
| 9 |
+
name: ENCODE + Roadmap Epigenomics (919 targets)
|
| 10 |
+
type: genomics
|
| 11 |
+
split: "held-out chromosomes (validation: chr6/7, test: chr8/9)"
|
| 12 |
+
metrics:
|
| 13 |
+
- name: AUROC (TF)
|
| 14 |
+
type: auc
|
| 15 |
+
value: 0.948
|
| 16 |
+
- name: AUPRC (TF)
|
| 17 |
+
type: average precision
|
| 18 |
+
value: 0.353
|
| 19 |
+
- name: AUROC (DNase)
|
| 20 |
+
type: auc
|
| 21 |
+
value: 0.907
|
| 22 |
+
- name: AUPRC (DNase)
|
| 23 |
+
type: average precision
|
| 24 |
+
value: 0.472
|
| 25 |
+
- name: AUROC (Histone)
|
| 26 |
+
type: auc
|
| 27 |
+
value: 0.850
|
| 28 |
+
- name: AUPRC (Histone)
|
| 29 |
+
type: average precision
|
| 30 |
+
value: 0.367
|
| 31 |
+
- name: AUROC (average)
|
| 32 |
+
type: auc
|
| 33 |
+
value: 0.929
|
| 34 |
+
- name: AUPRC (average)
|
| 35 |
+
type: average precision
|
| 36 |
+
value: 0.379
|
| 37 |
+
---
|
| 38 |
+
|
| 39 |
# DeepShape
|
| 40 |
|
| 41 |

|
|
|
|
| 45 |
DeepShape is built upon DeeperDeepSEA, a PyTorch-based deep learning model originally designed to predict chromatin features from DNA sequence alone as implemented in [Selene](https://www.nature.com/articles/s41592-019-0360-8).
|
| 46 |
|
| 47 |
https://github.com/ni-lab/DeepShape
|
| 48 |
+
|
| 49 |
+
## License
|
| 50 |
+
|
| 51 |
+
DeepShape is licensed under the MIT License. Portions of this software are derived from [Selene](https://www.nature.com/articles/s41592-019-0360-8), which is licensed under the Clear BSD License.
|
| 52 |
+
See the [LICENSE](./LICENSE) file for full details.
|