Nucleotide Transformer downstream task H3K4me3.
22 evaluations · 22 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: BPNet (large), trained from scratch (NT benchmark) | Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3 | 0.445 (± 0.049) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.049 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (large) on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (large)', column 'H3K4me3'; printed identically in Supplementary Table 7 |
| Configuration: BPNet (original), trained from scratch (NT benchmark) | Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3 | 0.445 (± 0.047) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.047 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (original) on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (original)', column 'H3K4me3'; printed identically in Supplementary Table 7 |
| Configuration: BPNet (X-large), trained from scratch (NT benchmark) | Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3 | 0.338 (± 0.076) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.076 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (X-large) on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K4me3'; printed identically in Supplementary Table 7 |
| Configuration: DNABERT-2, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.646 (± 0.008) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.008 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'DNABERT-2', column 'H3K4me3' |
| Configuration: Enformer, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.635 (± 0.019) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.019 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'Enformer', column 'H3K4me3' |
| Configuration: HyenaDNA-1KB, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.596 (± 0.015) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.015 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-1KB on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'HyenaDNA-1KB', column 'H3K4me3' |
| Configuration: HyenaDNA-32KB, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.603 (± 0.02) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.02 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-32KB on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'HyenaDNA-32KB', column 'H3K4me3' |
| Configuration: NT-1000G (2.5B), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.615 (± 0.017) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.017 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G (2.5B) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-1000G (2.5B)', column 'H3K4me3' |
| Configuration: NT-1000G (2.5B), probing (NT benchmark) | Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3 | 0.603 (± 0.018) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.018 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G (2.5B) on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (2.5B)', column 'H3K4me3' |
| Configuration: NT-1000G (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.609 (± 0.011) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.011 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G (500M) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-1000G (500M)', column 'H3K4me3' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3 | 0.592 (± 0.011) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.011 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G (500M) on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H3K4me3' |
| Configuration: NT 2.5B Randomly Initialized, trained from scratch (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.463 (± 0.023) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.023 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT 2.5B Randomly Initialized on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT 2.5B Randomly Initialized', column 'H3K4me3' |
| Configuration: NT 500M Randomly Initialized, trained from scratch (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.452 (± 0.031) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.031 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT 500M Randomly Initialized on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT 500M Randomly Initialized', column 'H3K4me3' |
| Configuration: NT-HumanRef (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.622 (± 0.013) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.013 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-HumanRef (500M) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-HumanRef (500M)', column 'H3K4me3' |
| Configuration: NT-HumanRef (500M), probing (NT benchmark) | Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3 | 0.594 (± 0.012) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.012 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-HumanRef (500M) on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-HumanRef (500M)', column 'H3K4me3' |
| Configuration: NT-Multispecies (2.5B), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.618 (± 0.015) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.015 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies (2.5B) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies (2.5B)', column 'H3K4me3' |
| Configuration: NT-Multispecies (2.5B), probing (NT benchmark) | Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3 | 0.604 (± 0.016) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.016 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies (2.5B) on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-Multispecies (2.5B)', column 'H3K4me3' |
| Configuration: NT-Multispecies-v2 (100M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.633 (± 0.015) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.015 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies-v2 (100M) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (100M)', column 'H3K4me3' |
| Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.64 (± 0.009) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies-v2 (250M) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K4me3' |
| Configuration: NT-Multispecies-v2 (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.636 (± 0.016) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.016 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies-v2 (500M) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (500M)', column 'H3K4me3' |
| Configuration: NT-Multispecies-v2 (50M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3 | 0.627 (± 0.013) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.013 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies-v2 (50M) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (50M)', column 'H3K4me3' |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3 | 0.432 (± 0.008) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.008 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRaw Probe on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'Raw Probe', column 'H3K4me3'; printed identically in Supplementary Table 7 |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.
Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified
Exact outcomes, predictions, identifiers and evaluator are connected.
Missing or unresolved evidence
Verified: Not verified
Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.
Missing or unresolved evidence
Verified: Not verified
A pinned recipe describes the inputs, environment and resource requirements.
Missing or unresolved evidence
Verified: Not verified
Separate data and exposure records support an independent test.
Missing or unresolved evidence
Verified: Not verified
Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.
No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.
A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population 17468 training and 776 test sequences, maximum length 1000 bp; human Context-only references | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) Supplementary Table 5 Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location Supplementary Table 5 Context-only references | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) Supplementary Table 5 Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Species Homo sapiens Context-only references | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) Supplementary Table 5 Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Split Tenfold cross-validation on the training set; test set as in Supplementary Table 5 Context-only references | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) Supplementary Table 5 Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Nucleotide Transformer downstream task H3K4me3. Context-only references | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) Supplementary Table 5 Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Name NT benchmark H3K4me3 Context-only references | Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) Supplementary Table 5 Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: lit-genomics-20261011-ntbench-data-h3k4me3