Model type
Frozen DNA encoder plus fitted logistic-regression pipeline
Pipeline
DNABERT-2 117M · frozen pair embeddings
This MFASS pipeline uses a frozen DNABERT-2 encoder with an assay-specific logistic-regression head. It is distinct from the base encoder and from end-to-end fine-tuning.
Sources
MFASS v2 run_dnabert2.py · run_dnabert2.py module documentation and recorded runner configurationHow it worksEvaluated pipeline
Schematic of the pinned MFASS configuration; this does not generalise to every member of the model family.
Sources
MFASS v2 pinned rewire artifacts · benchmarks/mfass/README.md, DNABERT-2 protocol; results/dnabert2-117m-frozen-pair-logreg.json, config at bee9133b83f3aedaf2bbb9013f1875515845607eUnderlying model: DNABERT-2. Results on this page belong to this pipeline and its evaluated settings.
At a glance
Biological inputs
Validated 170-bp assay-oriented reference/mutant pairs
Sources
MFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedureOutputs
MFASS splice-disruption probabilities from the fitted logistic head
Sources
MFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedureSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 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 Pipeline: DNABERT-2 117M · frozen pair embeddingsProtocol: MFASS v2Dataset: 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. |
How it works
Evaluated procedure
Validated 170-base reference and mutant sequences are embedded separately. Attention-mask means of final hidden states are combined as reference plus mutant-minus-reference. Standardisation and balanced L2 logistic regression are fitted only on the training arm.
Sources
MFASS v2 pinned rewire artifacts · benchmarks/mfass/README.md, DNABERT-2 protocol; results/dnabert2-117m-frozen-pair-logreg.json, config at bee9133b83f3aedaf2bbb9013f1875515845607eStrengths and limitations
Strengths supported by sources
- Separates the utility of a frozen representation from encoder fine-tuning and pins the checkpoint and head settings.
Sources
MFASS v2 pinned rewire artifacts · benchmarks/mfass/README.md, DNABERT-2 protocol; results/dnabert2-117m-frozen-pair-logreg.json, config at bee9133b83f3aedaf2bbb9013f1875515845607e
Limitations and conditions
- The result tests this short-context supervised pipeline. It does not establish how all DNABERT-2 adaptations or all foundation models perform.
Sources
MFASS v2 pinned rewire artifacts · benchmarks/mfass/README.md, DNABERT-2 protocol; results/dnabert2-117m-frozen-pair-logreg.json, config at bee9133b83f3aedaf2bbb9013f1875515845607e
Profile review details
Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed.
Stable record: rewire-model-dnabert2-117m-frozen-pair-logregSpecifications
Inputs, training, access and other details
Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | Frozen DNA encoder plus fitted logistic-regression pipelineSourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Architecture / procedure | Attention-mask mean pooling of last hidden states for reference and mutant sequences; concatenate reference embedding with mutant-minus-reference, scale features and fit balanced L2 logistic regression with C=0.1 on train rows only.SourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Biological inputs | Validated 170-bp assay-oriented reference/mutant pairsSourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Outputs | MFASS splice-disruption probabilities from the fitted logistic headSourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Parameters | 117M frozen DNABERT-2 encoder; the logistic head is a separate fitted component.SourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Training data / fitting | The encoder remains frozen; StandardScaler and logistic regression fit split-v2 training variants without test tuning.SourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Context limits | 170 bases per sequence; tokenizer truncation disabled.SourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Known versions / configuration | zhihan1996/DNABERT-2-117M; runner revision bee9133b83f3aedaf2bbb9013f1875515845607eSourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Access | Pinned public runner; model and tokenizer identities are validated against recorded artifact hashes.SourcesMFASS v2 run_dnabert2.py · run_dnabert2.py; module documentation, main() configuration and scoring procedure |
| Code licence | MIT for the Rewire runner at the reviewed revision. Upstream DNABERT-2: Apache 2.0. These are separate component licences.Sources (2)Rewire benchmark runner licence; MAGICS-LAB/DNABERT_2 LICENSE · LICENSE; complete MIT grant; upstream LICENSE |
| Weights licence | The official DNABERT-2-117M checkpoint repository carries Apache 2.0. The separately fitted logistic-regression artifact is not assigned an additional inferred licence.Sourceshuggingface.co/zhihan1996/DNABERT-2-117M LICENSE · LICENSE in official checkpoint repository |
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Schematic of the pinned MFASS configuration; this does not generalise to every member of the model family. Individual claims | MFASS v2 pinned rewire artifacts benchmarks/mfass/README.md, DNABERT-2 protocol; results/dnabert2-117m-frozen-pair-logreg.json, config at bee9133b83f3aedaf2bbb9013f1875515845607e Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Local imported data/benchmark-runs/mfass-v2.json; not the upstream repository or result-file hash |
| Diagram steps ["Assay-oriented sequence pair","Frozen DNABERT-2","Masked mean embeddings","Reference plus difference","Trained logistic head"] Individual claims | MFASS v2 pinned rewire artifacts benchmarks/mfass/README.md, DNABERT-2 protocol; results/dnabert2-117m-frozen-pair-logreg.json, config at bee9133b83f3aedaf2bbb9013f1875515845607e Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Local imported data/benchmark-runs/mfass-v2.json; not the upstream repository or result-file hash |
| Diagram title Evaluated pipeline Individual claims | MFASS v2 pinned rewire artifacts benchmarks/mfass/README.md, DNABERT-2 protocol; results/dnabert2-117m-frozen-pair-logreg.json, config at bee9133b83f3aedaf2bbb9013f1875515845607e Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Local imported data/benchmark-runs/mfass-v2.json; not the upstream repository or result-file hash |
| Model type Frozen DNA encoder plus fitted logistic-regression pipeline Individual claims | MFASS v2 run_dnabert2.py run_dnabert2.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure Attention-mask mean pooling of last hidden states for reference and mutant sequences; concatenate reference embedding with mutant-minus-reference, scale features and fit balanced L2 logistic regression with C=0.1 on train rows only. Individual claims | MFASS v2 run_dnabert2.py run_dnabert2.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence The official DNABERT-2-117M checkpoint repository carries Apache 2.0. The separately fitted logistic-regression artifact is not assigned an additional inferred licence. Individual claims | huggingface.co/zhihan1996/DNABERT-2-117M LICENSE LICENSE in official checkpoint repository Version: 7bce263b15377fc15361f52cfab88f8b586abda0 | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Validated 170-bp assay-oriented reference/mutant pairs Individual claims | MFASS v2 run_dnabert2.py run_dnabert2.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs MFASS splice-disruption probabilities from the fitted logistic head Individual claims | MFASS v2 run_dnabert2.py run_dnabert2.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters 117M frozen DNABERT-2 encoder; the logistic head is a separate fitted component. Individual claims | MFASS v2 run_dnabert2.py run_dnabert2.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Training data / fitting The encoder remains frozen; StandardScaler and logistic regression fit split-v2 training variants without test tuning. Individual claims | MFASS v2 run_dnabert2.py run_dnabert2.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e | source checked automated source review · 2026-09-16 Audit detailsPinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: source checked
5 source records and release history
- MFASS v2 pinned rewire artifacts · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
- MFASS v2 run_dnabert2.py · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
- Rewire benchmark runner licence · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
- MAGICS-LAB/DNABERT_2 LICENSE · Original source · f25bed9ee20db966dff39e5c1571249d04e36404
- huggingface.co/zhihan1996/DNABERT-2-117M LICENSE · Original source · 7bce263b15377fc15361f52cfab88f8b586abda0
Technical metadata and extraction receipts
Stable ID: rewire-model-dnabert2-117m-frozen-pair-logreg
- areas
- dna-genomes
- entity level
- method
- version
- bee9133b83f3aedaf2bbb9013f1875515845607e
- reported name
- DNABERT-2 117M · frozen pair embeddings
- historical missing metadata
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: evidence-reported-rewire-run-dnabert2; source locator: run_dnabert2.py; module documentation, main() configuration and scoring procedure | run_dnabert2.py module documentation and recorded runner configuration; ambiguities: None recorded