omegagenome-distilled-students

explcre/omegagenome-distilled-students

omegagenome-distilled-students is a machine learning model from explcre. Use it for the machine learning task on the model card, and read the license before you ship it in a product. The card lists the license as other.

Distilled student checkpoints from the OmegaGenome study (Science Advances). Code archive: https://doi.org/10.5281/zenodo.22805336 Two families of students, two teachers.

Downloads · 30 days

Access

Public

Updated Sep 25, 2026

Repo size

11.8 GB

Likes

Public

Hugging Face

Repo makeup

Click a slice to open those files.

.pth11.9 GB · 99%

At a glance

License: other
Access: Public
Created: Jun 28, 2026
Updated: Sep 25, 2026
SHA: 54eeb34c

Model card

From the Hugging Face model README

OmegaGenome Distilled Students

Distilled student checkpoints from the OmegaGenome study (Science Advances). Code archive: https://doi.org/10.5281/zenodo.22805336 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.

Licence

This repository contains two families of checkpoints with different upstream constraints:

folder	licence	why
`3seed_best_students/`, `carbon_bpnet_students/`	CC BY-NC-SA 4.0	distilled from teachers including NT-2.5B, released by InstaDeep under CC BY-NC-SA 4.0
`ntv3_kd_students/`, `regression/`	InstaDeep Open Model Licence v1.0	initialised from and distilled from NTv3, whose licence requires derived and distilled models to be non-commercial and released under the same licence

Both are for non-commercial research use. The OmegaGenome source code is separate and MIT-licensed (https://doi.org/10.5281/zenodo.22805336).

License: other
Created: Jun 28, 2026
Updated: Sep 25, 2026