Update model card for widewin-roadmap retrain (sparse H3K27ac)
Browse files
README.md
CHANGED
|
@@ -25,7 +25,7 @@ cropped for the heads (ChromBPNet-style "valid" geometry, so every output base
|
|
| 25 |
has a full real-sequence receptive field). The two channels are:
|
| 26 |
|
| 27 |
- **ch0 — DNase**: 5′ cut-sites (motif-sensitive, sharp).
|
| 28 |
-
- **ch1 — H3K27ac**: read
|
| 29 |
|
| 30 |
Each cell line gets its **own** main checkpoint (no FiLM, no cell embedding),
|
| 31 |
paired with a per-cell **frozen 2-channel `BiasNet`** (1024-bp, run on the
|
|
@@ -47,12 +47,17 @@ bias/
|
|
| 47 |
... (11 cells)
|
| 48 |
```
|
| 49 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 50 |
## Training
|
| 51 |
|
| 52 |
- **Window**: 2114-bp input → central 1024-bp profile crop, on roadmap DNase
|
| 53 |
peak summits.
|
| 54 |
- **Signals**: ch0 = per-bp 5′ DNase cut-site counts; ch1 = per-bp H3K27ac
|
| 55 |
-
|
| 56 |
- **Data**: ENCODE DNase + H3K27ac BAMs (SE/PE), fold-10 leave-chromosomes-out
|
| 57 |
split (chr11+chr21 held out).
|
| 58 |
- **Loss**: multinomial NLL on the per-bp 2-channel profile + MSE on log10 count
|
|
|
|
| 25 |
has a full real-sequence receptive field). The two channels are:
|
| 26 |
|
| 27 |
- **ch0 — DNase**: 5′ cut-sites (motif-sensitive, sharp).
|
| 28 |
+
- **ch1 — H3K27ac**: read signal (the active-enhancer histone mark).
|
| 29 |
|
| 30 |
Each cell line gets its **own** main checkpoint (no FiLM, no cell embedding),
|
| 31 |
paired with a per-cell **frozen 2-channel `BiasNet`** (1024-bp, run on the
|
|
|
|
| 47 |
... (11 cells)
|
| 48 |
```
|
| 49 |
|
| 50 |
+
> **Shipped weights (2026-06-04): the `roadmap` retrain** — trained on Roadmap
|
| 51 |
+
> DNase-summit peaks with the Roadmap-pipeline H3K27ac. Strongest per-cell DNase
|
| 52 |
+
> test-r and a functional H3K27ac channel; supersedes an earlier ENCODE-IDR-peak /
|
| 53 |
+
> full-coverage-H3K27ac variant.
|
| 54 |
+
|
| 55 |
## Training
|
| 56 |
|
| 57 |
- **Window**: 2114-bp input → central 1024-bp profile crop, on roadmap DNase
|
| 58 |
peak summits.
|
| 59 |
- **Signals**: ch0 = per-bp 5′ DNase cut-site counts; ch1 = per-bp H3K27ac
|
| 60 |
+
signal (Roadmap v2.1 pipeline).
|
| 61 |
- **Data**: ENCODE DNase + H3K27ac BAMs (SE/PE), fold-10 leave-chromosomes-out
|
| 62 |
split (chr11+chr21 held out).
|
| 63 |
- **Loss**: multinomial NLL on the per-bp 2-channel profile + MSE on log10 count
|