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
Enhancer recognition
Recognize enhancer sequence windows independent of quantitative activity.
Task definition
- Input granularity
- sequence/window
- Biological target
- enhancer presence
- Output representation
- binary label
- ML formulation
- classification
- Counting notes
- NR
Benchmark coverage
5 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)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
10 protocol units
| Protocol | Track | Split / subset | Comparability |
|---|---|---|---|
PROT-B03-ENHANCER-ANNOTATION-OFFICIAL-10-FOL-A1F324B3-A796D75D | enhancer_annotation NR | official 10-fold cross-validation enhancer annotation | same_table_comparable inference_budget |
PROT-B02-NT-HF-38A9E295D4E2564E | enhancers_types B02-TR03 | official tenfold cross-validation test folds enhancers_types | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-0D0BEF08F4BE0015 | enhancers_types B02-TR03 | official tenfold cross-validation test folds enhancers_types | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-6E474B8760917E0C | enhancers_types B02-TR03 | official tenfold cross-validation test folds enhancers_types | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-42A0F677CDC6800D | enhancers B02-TR03 | official tenfold cross-validation test folds enhancers | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-93D7D965ACDC7DCE | enhancers B02-TR03 | official tenfold cross-validation test folds enhancers | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-9B10421717B4FB63 | enhancers B02-TR03 | official tenfold cross-validation test folds enhancers | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-780CC1E9BC843A99 | enhancers B02-TR03 | official CSV row with 12 reported fold values; isolated from tenfold board enhancers | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-9BFF5ECC83FBBF0F | enhancers B02-TR03 | official CSV row with 12 reported fold values; isolated from tenfold board enhancers | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-F71C2E05E5F88948 | enhancers B02-TR03 | official CSV row with 12 reported fold values; isolated from tenfold board enhancers | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |