Nucleotide Transformer downstream task Enhancer types.
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 Enhancer types, probing Dataset: NT benchmark Enhancer types | 0.454 (± 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 sourceBPNet (large) on NT benchmark Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (large)', column 'Enhancer types'; printed identically in Supplementary Table 7 |
| Configuration: BPNet (original), trained from scratch (NT benchmark) | Protocol: NT benchmark Enhancer types, probing Dataset: NT benchmark Enhancer types | 0.449 (± 0.006) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (original) on NT benchmark Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (original)', column 'Enhancer types'; printed identically in Supplementary Table 7 |
| Configuration: BPNet (X-large), trained from scratch (NT benchmark) | Protocol: NT benchmark Enhancer types, probing Dataset: NT benchmark Enhancer types | 0.455 (± 0.012) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.012 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (X-large) on NT benchmark Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Enhancer types'; printed identically in Supplementary Table 7 |
| Configuration: DNABERT-2, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.476 (± 0.009) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'DNABERT-2', column 'Enhancer types' |
| Configuration: Enformer, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.573 (± 0.013) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.013 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'Enformer', column 'Enhancer types' |
| Configuration: HyenaDNA-1KB, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.441 (± 0.01) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-1KB on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'HyenaDNA-1KB', column 'Enhancer types' |
| Configuration: HyenaDNA-32KB, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.445 (± 0.009) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-32KB on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'HyenaDNA-32KB', column 'Enhancer types' |
| Configuration: NT-1000G (2.5B), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.469 (± 0.005) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.005 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G (2.5B) on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-1000G (2.5B)', column 'Enhancer types' |
| Configuration: NT-1000G (2.5B), probing (NT benchmark) | Protocol: NT benchmark Enhancer types, probing Dataset: NT benchmark Enhancer types | 0.439 (± 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-1000G (2.5B) on NT benchmark Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (2.5B)', column 'Enhancer types' |
| Configuration: NT-1000G (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.459 (± 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 Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-1000G (500M)', column 'Enhancer types' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark Enhancer types, probing Dataset: NT benchmark Enhancer types | 0.431 (± 0.005) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.005 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G (500M) on NT benchmark Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'Enhancer types' |
| Configuration: NT 2.5B Randomly Initialized, trained from scratch (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.225 (± 0.021) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.021 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT 2.5B Randomly Initialized on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT 2.5B Randomly Initialized', column 'Enhancer types' |
| Configuration: NT 500M Randomly Initialized, trained from scratch (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.215 (± 0.022) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.022 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT 500M Randomly Initialized on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT 500M Randomly Initialized', column 'Enhancer types' |
| Configuration: NT-HumanRef (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.477 (± 0.014) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.014 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-HumanRef (500M) on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-HumanRef (500M)', column 'Enhancer types' |
| Configuration: NT-HumanRef (500M), probing (NT benchmark) | Protocol: NT benchmark Enhancer types, probing Dataset: NT benchmark Enhancer types | 0.423 (± 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 Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-HumanRef (500M)', column 'Enhancer types' |
| Configuration: NT-Multispecies (2.5B), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.484 (± 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-Multispecies (2.5B) on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies (2.5B)', column 'Enhancer types' |
| Configuration: NT-Multispecies (2.5B), probing (NT benchmark) | Protocol: NT benchmark Enhancer types, probing Dataset: NT benchmark Enhancer types | 0.446 (± 0.007) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.007 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies (2.5B) on NT benchmark Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-Multispecies (2.5B)', column 'Enhancer types' |
| Configuration: NT-Multispecies-v2 (100M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.465 (± 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 (100M) on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (100M)', column 'Enhancer types' |
| Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.492 (± 0.01) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies-v2 (250M) on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Enhancer types' |
| Configuration: NT-Multispecies-v2 (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.498 (± 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 (500M) on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (500M)', column 'Enhancer types' |
| Configuration: NT-Multispecies-v2 (50M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types | 0.459 (± 0.006) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-Multispecies-v2 (50M) on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (50M)', column 'Enhancer types' |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark Enhancer types, probing Dataset: NT benchmark Enhancer types | 0.233 (± 0.004) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.004 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRaw Probe on NT benchmark Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'Raw Probe', column 'Enhancer types'; printed identically in Supplementary Table 7 |
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6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population 30000 training and 3000 test sequences, maximum length 400 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 Enhancer types. 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 Enhancer types 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-enhancer-types