OmegaGenome Distilled Students
Distilled student checkpoints from the OmegaGenome (NeurIPS 2026 revision) study. Two families of students, two teachers.
1. NTv3 single-track KD students (ntv3_kd_students/)
Small NTv3 students (8M / 100M) distilled per single genomic track from the NTv3-650M multitrack teacher (faithful recipe, 19,932 steps, cached teacher logits). Metric = per-track test Pearson r.
| track | assay | student | KD | base (no-KD) | teacher | d(KD-base) | % teacher |
|---|---|---|---|---|---|---|---|
| t0 | PRO-cap | 8M | 0.4474 | 0.3801 | 0.5344 | +0.0673 | 84% |
| t3 | PRO-cap | 8M | 0.4485 | 0.4125 | 0.5671 | +0.0360 | 79% |
| t11 | eCLIP | 8M | 0.6142 | 0.5839 | 0.6886 | +0.0303 | 89% |
| t12 | ATAC | 8M | 0.7556 | 0.7469 | 0.8326 | +0.0087 | 91% |
| t14 | eCLIP | 8M | 0.4103 | 0.3929 | 0.4782 | +0.0174 | 86% |
| t18 | polyA-RNA | 8M | 0.6329 | 0.5933 | 0.7203 | +0.0396 | 88% |
| t20 | polyA-RNA | 8M | 0.6366 | 0.6089 | 0.6992 | +0.0277 | 91% |
| t33 | Histone | 100M | 0.8887 | 0.8828 | 0.9143 | +0.0059 | 97% |
All d>0 (KD beats the matched no-distillation baseline). t33 (Histone) is the 100M capacity-lever result
(the 8M ties on t33; 100M opens headroom so KD wins). Files: ntv3_kd_students/{8m,100m}/t<N>_kd.pth
(raw state_dict).
2. Carbon-3B BPNet KD students (carbon_bpnet_students/)
Tiny BPNet students distilled from Carbon-3B LoRA teachers on the NT18 classification tasks; best HP config per task (selected by validation MCC from the HP grid). Metric = MCC.
| task | best_val_mcc | best_test_mcc |
|---|---|---|
| H2AFZ | 0.5233 | 0.4919 |
| H3K27ac | 0.4896 | 0.4817 |
| H3K27me3 | 0.6012 | 0.5899 |
| H3K36me3 | 0.6176 | 0.5634 |
| H3K4me1 | 0.4931 | 0.4718 |
| H3K4me2 | 0.5926 | 0.5481 |
| H3K4me3 | 0.6842 | 0.6319 |
| H3K9ac | 0.5614 | 0.4954 |
| H3K9me3 | 0.4092 | 0.3972 |
| H4K20me1 | 0.6360 | 0.6211 |
| enhancers | 0.5151 | 0.4975 |
| enhancers_types | 0.4831 | 0.4688 |
| promoter_all | 0.7541 | 0.7415 |
| promoter_no_tata | 0.7487 | 0.7305 |
| promoter_tata | 0.8544 | 0.8308 |
| splice_sites_acceptors | 0.9060 | 0.8907 |
| splice_sites_all | 0.8853 | 0.8779 |
| splice_sites_donors | 0.9337 | 0.9025 |
Files: carbon_bpnet_students/<task>.pt (raw state_dict).
Interim selection from the ongoing HP search; "best" config may shift as the grid completes. NTv3 100M near-miss students (t11/t18/t14/t0/t3) to follow once trained.