GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
Transcription factor prediction (mouse), dataset 3. Scored with MCC on GUE Transcription factor prediction (mouse), 3. Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.
Overview
Transcription factor prediction (mouse), dataset 3. Scored with MCC on GUE Transcription factor prediction (mouse), 3. Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- DNABERT-2 (further pre-trained on GUE) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- DNABERT-2 on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- DNABERT (3-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- DNABERT (4-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- DNABERT (5-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- NT-2500M-1000g on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- NT-2500M-multi on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- NT-500M-1000g on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- NT-500M-human on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
mcc (percent) · Higher values are better for this metric.
Every method GUE reports on Transcription factor prediction (mouse), dataset 3, scored with MCC on GUE Transcription factor prediction (mouse), 3.
Evaluation protocol · GUE Transcription factor prediction (mouse), 3 (GUE split)
- DNABERT (3-mer) · Configuration · Author-reported evaluation55.40
- DNABERT (4-mer) · Configuration · Author-reported evaluation51.79
- DNABERT (5-mer) · Configuration · Author-reported evaluation49.92
- DNABERT (6-mer) · Configuration · Author-reported evaluation44.89
- NT-500M-human · Configuration · Author-reported evaluation29.17
- NT-500M-1000g · Configuration · Author-reported evaluation33.07
- NT-2500M-1000g · Configuration · Author-reported evaluation42.25
- NT-2500M-multi · Configuration · Author-reported evaluation69.44
- DNABERT-2 · Configuration · Author-reported evaluation66.47
- DNABERT-2 (further pre-trained on GUE) · Configuration · Author-reported evaluation73.49
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 12, row(Transcription factor prediction (mouse))Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| DNABERT (3-mer) · Configuration | 55.40 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (3-mer)), column(Transcription factor prediction (mouse) 3) |
| DNABERT (4-mer) · Configuration | 51.79 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (4-mer)), column(Transcription factor prediction (mouse) 3) |
| DNABERT (5-mer) · Configuration | 49.92 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (5-mer)), column(Transcription factor prediction (mouse) 3) |
| DNABERT (6-mer) · Configuration | 44.89 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (mouse) 3) |
| NT-500M-human · Configuration | 29.17 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(NT-500M-human), column(Transcription factor prediction (mouse) 3) |
| NT-500M-1000g · Configuration | 33.07 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(NT-500M-1000g), column(Transcription factor prediction (mouse) 3) |
| NT-2500M-1000g · Configuration | 42.25 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(NT-2500M-1000g), column(Transcription factor prediction (mouse) 3) |
| NT-2500M-multi · Configuration | 69.44 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(NT-2500M-multi), column(Transcription factor prediction (mouse) 3) |
| DNABERT-2 · Configuration | 66.47 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT-2), column(Transcription factor prediction (mouse) 3) |
| DNABERT-2 (further pre-trained on GUE) · Configuration | 73.49 percent | Not reported | Author-reported evaluation · source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT-2♦), column(Transcription factor prediction (mouse) 3) |
Scope and limitations
- Author-reported numbers, source checked but not independently reproduced.
- Scores are MCC, except Covid variant classification which is F1, both on a 0 to 100 scale.
- The diamond entry is DNABERT-2 with further pre-training on the GUE training sets, so it is not directly comparable to the others.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 10 evaluations · 10 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| DNABERT-2 (further pre-trained on GUE) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: DNABERT-2 (further pre-trained on GUE)Task: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 73.49% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT-2♦), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| DNABERT-2 on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: DNABERT-2Task: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 66.47% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT-2), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| DNABERT (3-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: DNABERT (3-mer)Task: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 55.40% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (3-mer)), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| DNABERT (4-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: DNABERT (4-mer)Task: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 51.79% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (4-mer)), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| DNABERT (5-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: DNABERT (5-mer)Task: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 49.92% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (5-mer)), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: DNABERT (6-mer)Task: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 44.89% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(DNABERT (6-mer)), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| NT-2500M-1000g on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: NT-2500M-1000gTask: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 42.25% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(NT-2500M-1000g), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| NT-2500M-multi on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: NT-2500M-multiTask: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 69.44% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(NT-2500M-multi), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| NT-500M-1000g on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: NT-500M-1000gTask: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 33.07% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(NT-500M-1000g), column(Transcription factor prediction (mouse) 3) Source checking is not independent reproduction. |
| NT-500M-human on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3 Configuration: NT-500M-humanTask: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3Dataset subset: GUE Transcription factor prediction (mouse), 3 (GUE split) Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12. Author-reported evaluation · Evaluation metadata: source checked | ||
| 29.17% mcc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Table 6, row(NT-500M-human), column(Transcription factor prediction (mouse) 3) Source checking is not 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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-gue Individual claims | DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes Table 12, row(Transcription factor prediction (mouse)) Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: gue-association-transcription-factor-prediction-mouse-3 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Technical metadata and extraction receipts
Stable ID: gue-task-transcription-factor-prediction-mouse-3
- areas
- dna-genomes
- tasks
- Transcription factor prediction (mouse), dataset 3
- metric
- MCC
- metric direction
- higher
- dataset
- GUE Transcription factor prediction (mouse), 3
- protocol
- Fine-tuned on the GUE training split, scored on its test split. Split sizes are in Table 12.
- source locator
- Table 12, row(Transcription factor prediction (mouse))
- comparison panels
- id: gue-panel-transcription-factor-prediction-mouse-3; title: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3; protocol id: gue-task-transcription-factor-prediction-mouse-3; dataset id: gue-dataset-gue-transcription-factor-prediction-mouse-3; metric: mcc; unit: percent; direction: higher; result ids: gue-result-dnabert-3-mer-transcription-factor-prediction-mouse-3-mcc; gue-result-dnabert-4-mer-transcription-factor-prediction-mouse-3-mcc; gue-result-dnabert-5-mer-transcription-factor-prediction-mouse-3-mcc; gue-result-dnabert-6-mer-transcription-factor-prediction-mouse-3-mcc; gue-result-nt-500m-human-transcription-factor-prediction-mouse-3-mcc; gue-result-nt-500m-1000g-transcription-factor-prediction-mouse-3-mcc; gue-result-nt-2500m-1000g-transcription-factor-prediction-mouse-3-mcc; gue-result-nt-2500m-multi-transcription-factor-prediction-mouse-3-mcc; gue-result-dnabert-2-transcription-factor-prediction-mouse-3-mcc; gue-result-dnabert-2-further-pre-trained-on-gue-transcription-factor-prediction-mouse-3-mcc; source ids: evidence-expansion-gue-49300ace; source locator: Table 12, row(Transcription factor prediction (mouse)); context: Every method GUE reports on Transcription factor prediction (mouse), dataset 3, scored with MCC on GUE Transcription factor prediction (mouse), 3.; caveats: Author-reported numbers, source checked but not independently reproduced.; Scores are MCC, except Covid variant classification which is F1, both on a 0 to 100 scale.; The diamond entry is DNABERT-2 with further pre-training on the GUE training sets, so it is not directly comparable to the others.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: GUE
- subject: GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: part of discovery-benchmark-gue
- benchmark: DNABERT-2 (further pre-trained on GUE) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: DNABERT-2 on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: DNABERT (3-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: DNABERT (4-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: DNABERT (5-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: DNABERT (6-mer) on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: NT-2500M-1000g on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: NT-2500M-multi on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: NT-500M-1000g on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3
- benchmark: NT-500M-human on GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3