Genome Understanding Evaluation (GUE)
28 datasets/tasks in the native packaging; mapped here to five task families.
1 benchmark-wide protocols · 10 benchmark-wide rows (not a task subtotal)D1 · Sequence understanding & regulation
Promoter recognition
Recognize promoter sequence windows; promoter activity is counted separately under D3.
Task definition
- Input granularity
- sequence/window
- Biological target
- promoter presence or type
- Output representation
- binary/multiclass label
- ML formulation
- classification
- Counting notes
- NR
Benchmark coverage
6 benchmarks cover this task
Nucleotide Transformer benchmark
Eighteen downstream tasks are benchmark instances, not eighteen unique task families.
67 benchmark-wide protocols · 821 benchmark-wide rows (not a task subtotal)GenBench
Framework and dataset suite; native task count follows current release documentation.
0 benchmark-wide protocols · 0 benchmark-wide rows (not a task subtotal)Genomic Benchmarks
Widely reused classification datasets; simple random-style splits can inflate biological generalization.
0 benchmark-wide protocols · 0 benchmark-wide rows (not a task subtotal)Benchmarking DNA foundation models for genomic and genetic tasks
One-time benchmark study rather than a maintained benchmark suite.
6 benchmark-wide protocols · 8 benchmark-wide rows (not a task subtotal)OmniGenBench
Meta-suite packaging RGB, BEACON, GUE, Genomic Benchmarks and PGB; native_task_count=5 suites, not the sum of their downstream tasks.
0 benchmark-wide protocols · 0 benchmark-wide rows (not a task subtotal)Evaluation protocols
9 protocol units
| Protocol | Track | Split / subset | Comparability |
|---|---|---|---|
PROT-B02-NT-HF-285B11CF193A76F9 | promoter_tata B02-TR02 | official tenfold cross-validation test folds promoter_tata | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-E001D1E02DE3C282 | promoter_tata B02-TR02 | official tenfold cross-validation test folds promoter_tata | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-9B5E54F3949755BB | promoter_tata B02-TR02 | official tenfold cross-validation test folds promoter_tata | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-ED33DF72216BFAB1 | promoter_all B02-TR02 | official tenfold cross-validation test folds promoter_all | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-9D92D53E79151944 | promoter_all B02-TR02 | official tenfold cross-validation test folds promoter_all | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-A7C4A01EC6680F19 | promoter_all B02-TR02 | official tenfold cross-validation test folds promoter_all | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-EA319DDE4E394B6E | promoter_no_tata B02-TR02 | official tenfold cross-validation test folds promoter_no_tata | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-3E9437F665A4D0E3 | promoter_no_tata B02-TR02 | official tenfold cross-validation test folds promoter_no_tata | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-E0C57528CBCF31BD | promoter_no_tata B02-TR02 | official tenfold cross-validation test folds promoter_no_tata | official_board_comparable external_data_policy;inference_budget |