lucapinello commited on
Commit
c7910ea
·
verified ·
1 Parent(s): 2654c05

Update model card for widewin-roadmap retrain (sparse H3K27ac)

Browse files
Files changed (1) hide show
  1. README.md +7 -2
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 coverage (the histone mark's broad pile-up signal).
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
- read coverage.
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