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)D1 · Sequence understanding & regulation
Histone-mark prediction
Predict histone-mark assay signal from sequence.
Task definition
- Input granularity
- long sequence/window
- Biological target
- histone modification signal
- Output representation
- continuous track
- ML formulation
- regression
- Counting notes
- NR
Benchmark coverage
3 benchmarks cover this task
DNALongBench
Long-range genomic tasks; exact sequence length and cell-type packaging vary by track.
2 benchmark-wide protocols · 6 benchmark-wide rows (not a task subtotal)GenoArmory
Adversarial robustness wrapper over eight GUE histone-mark datasets; four attack families and three defense strategies are evaluation regimes, not new biological task families.
0 benchmark-wide protocols · 0 benchmark-wide rows (not a task subtotal)Evaluation protocols
41 protocol units
| Protocol | Track | Split / subset | Comparability |
|---|---|---|---|
PROT-B03-HISTONE-MODIFICATION-OFFICIAL-420-7-18D1B1D9-AB87277A | histone_modification NR | official 420,713/70,801/120,567 split histone modification | same_table_comparable inference_budget |
PROT-B03-CPG-METHYLATION-OFFICIAL-743-095-10-F4FB3847-99DDAE0F | cpg_methylation NR | official 743,095/109,717/106,227 split cpg methylation | same_table_comparable inference_budget |
PROT-B02-NT-HF-BA04826A801395E7 | H3K9me3 B02-TR06 | official tenfold cross-validation test folds H3K9me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-62CBAA925FD0880A | H3K9me3 B02-TR06 | official tenfold cross-validation test folds H3K9me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-60A451C799B97E03 | H3K9me3 B02-TR06 | official tenfold cross-validation test folds H3K9me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-5A96826DDDE6E31E | H3K4me2 B02-TR06 | official tenfold cross-validation test folds H3K4me2 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-00E70CBC4F34D686 | H3K4me2 B02-TR06 | official tenfold cross-validation test folds H3K4me2 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-D472A4DD1EA67F7E | H3K4me2 B02-TR06 | official tenfold cross-validation test folds H3K4me2 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-A91A084112FF9A32 | H2AFZ B02-TR06 | official tenfold cross-validation test folds H2AFZ | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-FA5900E4DD5D8E94 | H2AFZ B02-TR06 | official tenfold cross-validation test folds H2AFZ | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-4857A0D798FBD04D | H2AFZ B02-TR06 | official tenfold cross-validation test folds H2AFZ | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-73E94947FFB9DA98 | H3K27me3 B02-TR06 | official tenfold cross-validation test folds H3K27me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-C165144F548D553E | H3K27me3 B02-TR06 | official tenfold cross-validation test folds H3K27me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-F6C100D4F6888DA0 | H3K27me3 B02-TR06 | official tenfold cross-validation test folds H3K27me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-E0B0D2C56965AB32 | H3K36me3 B02-TR06 | official tenfold cross-validation test folds H3K36me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-5943CFA2B6032C87 | H3K36me3 B02-TR06 | official tenfold cross-validation test folds H3K36me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-5011D45544AF1180 | H3K36me3 B02-TR06 | official tenfold cross-validation test folds H3K36me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-84F379F4C9866CB3 | H3K27ac B02-TR06 | official tenfold cross-validation test folds H3K27ac | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-323E9FCD49B43611 | H3K27ac B02-TR06 | official tenfold cross-validation test folds H3K27ac | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-E36FBF3F175453DB | H3K27ac B02-TR06 | official tenfold cross-validation test folds H3K27ac | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-8D48D582CE11AC95 | H3K4me3 B02-TR06 | official tenfold cross-validation test folds H3K4me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-B75B6DE89F0AD90A | H3K4me3 B02-TR06 | official tenfold cross-validation test folds H3K4me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-38160C93A786C48F | H3K4me3 B02-TR06 | official tenfold cross-validation test folds H3K4me3 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-BFAF051E02BBE968 | H4K20me1 B02-TR06 | official tenfold cross-validation test folds H4K20me1 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-4FF72F8C292562E6 | H4K20me1 B02-TR06 | official tenfold cross-validation test folds H4K20me1 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-88F7B3DAACA2DA45 | H4K20me1 B02-TR06 | official tenfold cross-validation test folds H4K20me1 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-CA6990A54A326808 | H3K4me1 B02-TR06 | official tenfold cross-validation test folds H3K4me1 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-90622A7F6855CDB0 | H3K4me1 B02-TR06 | official tenfold cross-validation test folds H3K4me1 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-2BDAEBE21A3140A0 | H3K4me1 B02-TR06 | official tenfold cross-validation test folds H3K4me1 | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-452816D2253B3EA7 | H3K9ac B02-TR06 | official tenfold cross-validation test folds H3K9ac | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-D95AC35B14C9E6D2 | H3K9ac B02-TR06 | official tenfold cross-validation test folds H3K9ac | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-23926116A148178F | H3K9ac B02-TR06 | official tenfold cross-validation test folds H3K9ac | official_board_comparable external_data_policy;inference_budget |
PROT-B02-NT-HF-FC56F9229B00DC9E | H4K20me1 B02-TR06 | official CSV row with 13 reported fold values; isolated from tenfold board H4K20me1 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-C394583E33B91114 | H4K20me1 B02-TR06 | official CSV row with 13 reported fold values; isolated from tenfold board H4K20me1 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-045BA8FF78EF67CE | H4K20me1 B02-TR06 | official CSV row with 13 reported fold values; isolated from tenfold board H4K20me1 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-110E6351EAC1B63A | H3K9me3 B02-TR06 | official CSV row with 14 reported fold values; isolated from tenfold board H3K9me3 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-1EC745E13661A9EE | H3K9me3 B02-TR06 | official CSV row with 14 reported fold values; isolated from tenfold board H3K9me3 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-4BF556958F957526 | H3K9me3 B02-TR06 | official CSV row with 14 reported fold values; isolated from tenfold board H3K9me3 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-409894AB52472E9C | H3K9me3 B02-TR06 | official CSV row with 9 reported fold values; isolated from tenfold board H3K9me3 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-19F8E62C504D1CE1 | H3K9me3 B02-TR06 | official CSV row with 9 reported fold values; isolated from tenfold board H3K9me3 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |
PROT-B02-NT-HF-DBBAB154E33BECD0 | H3K9me3 B02-TR06 | official CSV row with 9 reported fold values; isolated from tenfold board H3K9me3 | insufficient_protocol_detail nonstandard fold-array length;external_data_policy;inference_budget |