DNABERT-2 117M · frozen pair embeddings on MFASS v2
Evaluation procedure
Masked mean of frozen last hidden states for 170 bp reference and mutant sequences; concatenate reference and mutant-minus-reference embeddings; fixed balanced L2 logistic head trained only on the MFASS training split.
- Model
- DNABERT-2 117M · frozen pair embeddings
- Benchmark
- MFASS v2
- Dataset
- MFASS v2 eligible assay cohort
- origin
- Rewire evaluation
- configuration
- bee9133b83f3aedaf2bbb9013f1875515845607e
- protocol id
- mfass-v2
- dataset version
- bee9133b83f3aedaf2bbb9013f1875515845607e
- split
- split-v2.tsv
- population
- 8324/8324
- inputs
- Not reported
- adaptation
- Not reported
- metric implementation
- Not reported
- aggregation
- Not reported
- budget
- Not reported
Metadata review: reproduced. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-16-d74d282221a9 · 1 evaluation · 3 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| DNABERT-2 117M · frozen pair embeddings on MFASS v2 Model: DNABERT-2 117M · frozen pair embeddings · Benchmark: MFASS v2 · Dataset: MFASS v2 eligible assay cohort Masked mean of frozen last hidden states for 170 bp reference and mutant sequences; concatenate reference and mutant-minus-reference embeddings; fixed balanced L2 logistic head trained only on the MFASS training split. Rewire evaluation · Evaluation metadata: reproduced | ||
| 0.5500324040216661 auroc Unit: fraction · Direction: higher | Uncertainty: Point estimate; see paired-comparison artifacts. Coverage (scored/eligible): 8324/8324 | reproducedMFASS v2 pinned rewire artifacts · benchmarks/mfass/results/dnabert2-117m-frozen-pair-logreg.json :: auroc Source checking is not independent reproduction. |
| 0.04508654312652131 average_precision Unit: fraction · Direction: higher | Uncertainty: Point estimate; see paired-comparison artifacts. Coverage (scored/eligible): 8324/8324 | reproducedMFASS v2 pinned rewire artifacts · benchmarks/mfass/results/dnabert2-117m-frozen-pair-logreg.json :: average_precision Source checking is not independent reproduction. |
| 0.03 precision_at_100 Unit: fraction · Direction: higher | Uncertainty: Point estimate; see paired-comparison artifacts. Coverage (scored/eligible): 8324/8324 | reproducedMFASS v2 pinned rewire artifacts · benchmarks/mfass/results/dnabert2-117m-frozen-pair-logreg.json :: precision_at_100 Source checking is not independent reproduction. |
Sources and history
Release 2026-09-16-d74d282221a9 · Record review: reproduced
- MFASS v2 pinned rewire artifacts · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
Technical metadata and extraction receipts
Stable ID: rewire-evaluation-dnabert2-117m-frozen-pair-logreg
- areas
- dna-genomes
- origin
- rewire_run
- protocol
- Masked mean of frozen last hidden states for 170 bp reference and mutant sequences; concatenate reference and mutant-minus-reference embeddings; fixed balanced L2 logistic head trained only on the MFASS training split.
- version
- bee9133b83f3aedaf2bbb9013f1875515845607e
- run url
- /benchmarks/runs/mfass-v2/
- comparison
- protocol id: mfass-v2; dataset version: bee9133b83f3aedaf2bbb9013f1875515845607e; split: split-v2.tsv; population: 8324/8324; inputs: Not reported; adaptation: Not reported; metric implementation: Not reported; aggregation: Not reported; budget: Not reported
- coverage
- 8324/8324
- missing metadata
- paired comparison: Refer to paired bootstrap artifacts; marginal scores are not paired comparisons.
Related records
- model: DNABERT-2 117M · frozen pair embeddings
- benchmark: MFASS v2
- dataset: MFASS v2 eligible assay cohort
- evaluation: DNABERT-2 117M · frozen pair embeddings · auroc
- evaluation: DNABERT-2 117M · frozen pair embeddings · average_precision
- evaluation: DNABERT-2 117M · frozen pair embeddings · precision_at_100