Model type
Masked-token DNA transformer encoder
Configuration
DNABERT-2 (probed)
DNABERT-2 learns DNA representations that can be adapted to genomic prediction tasks.
Sources (3)
MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0How it worksDNABERT-2 workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources (3)
MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0Overview
Inputs
DNA sequence tokenized with the supplied tokenizer.
Outputs
Token representations and, after a specified adaptation, task predictions.
Access
Official project documentation and implementation: https://github.com/MAGICS-LAB/DNABERT_2
Sources (3)
MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0limited source coverage · Automated source review, 2026-09-23. All specifications and missing details
Evaluations and results
22 evaluations · 22 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.757 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive GM12878 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-AUROC-GM12878) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.763 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive H1ESC peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-AUROC-H1ESC) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.65 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive HEPG2 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-AUROC-HEPG2) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.729 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive IMR90 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-AUROC-IMR90) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.721 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive K562 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-AUROC-K562) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.395 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank correlation with measured accessibility among positive GM12878 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-SPEARMAN-GM12878) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.584 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank correlation with measured accessibility among positive H1ESC peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-SPEARMAN-H1ESC) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.357 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank correlation with measured accessibility among positive HEPG2 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-SPEARMAN-HEPG2) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.275 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank correlation with measured accessibility among positive IMR90 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-SPEARMAN-IMR90) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.483 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank correlation with measured accessibility among positive K562 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed DNABERT-2), column(CA-SPEARMAN-K562) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.371 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 (probed) on DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy Classify which of five cell lines a accessible element belongs to. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed DNABERT-2), column(CTS-ACC) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.652 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 (probed) on DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878 One-against-rest AUROC for GM12878 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed DNABERT-2), column(CTS-GM12878) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.757 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC One-against-rest AUROC for H1ESC accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed DNABERT-2), column(CTS-H1ESC) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.762 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 (probed) on DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2 One-against-rest AUROC for HEPG2 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed DNABERT-2), column(CTS-HEPG2) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.691 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 (probed) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 One-against-rest AUROC for IMR90 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed DNABERT-2), column(CTS-IMR90) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval CTS-K562: Cell-type-specific element classification, K562 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.691 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 (probed) on DART-Eval CTS-K562: Cell-type-specific element classification, K562 One-against-rest AUROC for K562 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed DNABERT-2), column(CTS-K562) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Dataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) | 0.847 absolute_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 (probed) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 3, row(DNABERT-2), column(probed absolute_accuracy) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Dataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) | 0.943 paired_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 (probed) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 3, row(DNABERT-2), column(probed paired_accuracy) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC Dataset subset: Chromatin QTLs in African LCLs (DART-Eval split) | 0.502 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceScore the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African DNABERT-2), column(probed auroc) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r Dataset subset: Chromatin QTLs in African LCLs (DART-Eval split) | 0.007 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceScore the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African DNABERT-2), column(probed pearson_r) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC Dataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split) | 0.476 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceScore the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban DNABERT-2), column(probed auroc) |
| Configuration: DNABERT-2 (probed) | Task: DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r Dataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split) | 0.024 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceScore the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban DNABERT-2), column(probed pearson_r) |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
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How it works, versions and access
Related profile: DNABERT-2. This page retains the exact record and its evaluation context.
This configuration
DNA language model evaluated by the DART-Eval authors in the probed setting.
- record
- DNABERT-2 (probed)
- configuration
- Not reported
- entity type
- Configuration
How it works
How it works
DNABERT-2 merges recurring DNA substrings into byte-pair tokens, then processes those tokens with a masked-language-model transformer. ALiBi supplies distance-dependent attention biases, while FlashAttention changes how attention is computed. The resulting contextual embeddings need an explicit pooling rule and prediction head for a downstream task.
Sources (3)
MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0Versions and reproducibility
DNABERT-2-117M model card and official DNABERT_2 implementation. ALiBi permits inference beyond the pretraining sequence length, subject to attention/memory cost; this does not establish unlimited biological context or validated accuracy at arbitrary lengths.
Sources (3)
MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- The released model supports embedding extraction and task-specific fine-tuning.
Sources (3)
MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0
Limitations and conditions
- An embedding model alone is not the same evaluated pipeline as frozen embeddings followed by logistic regression. Tokenization and pooling choices must be preserved.
Sources (3)
MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0
Profile review details
Follow-up review of Reference checkpoint, Context limits, Training cutoff, Further pretraining. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied.
Stable record: discovery-model-dnabert-2Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-23. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | Masked-token DNA transformer encoderSources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Architecture | BERT-style DNA encoder with byte-pair tokenization, ALiBi relative attention biases and FlashAttention; task heads and pooling are separately configured.Sources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Inputs | DNA sequence tokenized with the supplied tokenizer.Sources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Outputs | Token representations and, after a specified adaptation, task predictions.Sources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Parameters | 117 million for DNABERT-2-117M; family names do not establish a particular checkpoint.Sources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Known versions | DNABERT-2-117M model card and official DNABERT_2 implementation.Sources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Training data | The paper describes a 32.49-billion-base corpus covering 135 species in six groups, alongside a 2.75-billion-base human corpus. Further GUE-domain pretraining is a separately reported model variant.Sources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Training cutoff | Section4.1 identifies the human and 135-species corpora but does not establish a latest-sequence deposition date. The model repository revision is not a training-data cutoff. · Not reported in inspected sourcesSourcesdnabert2 paper v2: primary artifact · Section4.1; Table11 |
| Context limits | The paper describes pretraining on 700-base sequences and evaluates 5,000–10,000-base GUE+ inputs after fine-tuning. This does not establish frozen-model accuracy at those lengths; tokenisation, truncation and adaptation must be specified.Sourcesdnabert2 paper v2: primary artifact · Section5.4 Results on GUE+, printed p10; Table2 input lengths |
| Weights licence | The official zhihan1996/DNABERT-2-117M checkpoint repository carries Apache-2.0 in its pinned LICENSE. This does not assign terms to a separately fitted downstream predictor.Sources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Access | Official project documentation and implementation: https://github.com/MAGICS-LAB/DNABERT_2Sources (3)MAGICS-LAB/DNABERT_2: README.md; MAGICS-LAB/DNABERT_2: LICENSE; dnabert2: Primary paper PDF · DNABERT-2 paper Sections 3.2, 4.1 and 5.2 (Further Pre-Training); official model card and implementation README; official DNABERT-2-117M checkpoint LICENSE at revision 7bce263b15377fc15361f52cfab88f8b586abda0 |
| Code licence | Apache-2.0SourcesMAGICS-LAB/DNABERT_2: LICENSE · LICENSE: licence text |
| Reference checkpoint | DNABERT-2-117M: Hugging Face revision 7bce263b15377fc15361f52cfab88f8b586abda0. Its pytorch_model.bin has registry-reported SHA-256 7ff39ec77a484dd01070a41bfd6e95cdd7247bec80fe357ab43a4be33687aeba. The weight file was not downloaded for this review.Sourcesdnabert2 release: primary artifact · sha; siblings[pytorch_model.bin].lfs.sha256 |
| Further pretraining | The diamond-marked DNABERT-2 variant receives additional masked-language-model training on GUE training sets. It must be distinguished from the base pretrained model in comparisons.Sourcesdnabert2 paper v2: primary artifact · Section5.2FurtherPreTraining; Table3caption |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: family discovery-model-dnabert-2 Individual claims | DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA DART-Eval Table 1 (DNABERT-2, 117M) and adaptation-specific result tables; source-labelled configuration DNABERT-2 (probed) | Existing reviewed locator: Table 1, row(DNABERT-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2412.05430v1 | source checked automated source review · 2026-09-23 Audit detailsSource review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Official paper fixes backbone identity and separates fine-tuning/probing/zero-shot conditions. Family link does not pool scores. Field: Claim: model-evaluation-identity-4cc31fb8a10bdfaa2785 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: family discovery-model-dnabert-2 Individual claims | MAGICS-LAB/DNABERT_2: README.md DART-Eval Table 1 (DNABERT-2, 117M) and adaptation-specific result tables; source-labelled configuration DNABERT-2 (probed) | Existing reviewed locator: Table 1, row(DNABERT-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: f25bed9ee20db966dff39e5c1571249d04e36404 | source checked automated source review · 2026-09-23 Audit detailsSource review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Official paper fixes backbone identity and separates fine-tuning/probing/zero-shot conditions. Family link does not pool scores. Field: Claim: model-evaluation-identity-4cc31fb8a10bdfaa2785 Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: source checked
1 source records and release history
- DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Original source · 2412.05430v1
Technical metadata and extraction receipts
Stable ID: dart-eval-method-dnabert-2-probed
- areas
- dna-genomes
- source locator
- Table 1, row(DNABERT-2)
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- family: DNABERT-2
- model: DNABERT-2 (probed) on DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives
- model: DNABERT-2 (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- model: DNABERT-2 (probed) on DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives
- model: DNABERT-2 (probed) on DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives
- model: DNABERT-2 (probed) on DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives
- model: DNABERT-2 (probed) on DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only
- model: DNABERT-2 (probed) on DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only
- model: DNABERT-2 (probed) on DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only
- model: DNABERT-2 (probed) on DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only
- model: DNABERT-2 (probed) on DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only
- model: DNABERT-2 (probed) on DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy
- model: DNABERT-2 (probed) on DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878
- model: DNABERT-2 (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- model: DNABERT-2 (probed) on DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2
- model: DNABERT-2 (probed) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90
- model: DNABERT-2 (probed) on DART-Eval CTS-K562: Cell-type-specific element classification, K562
- model: DNABERT-2 (probed) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy
- model: DNABERT-2 (probed) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy
- model: DNABERT-2 (probed) on DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC
- model: DNABERT-2 (probed) on DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r
- model: DNABERT-2 (probed) on DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC
- model: DNABERT-2 (probed) on DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r
- subject: DNABERT-2 (probed): family DNABERT-2