Nucleotide Transformer downstream task Promoter all.
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 Promoter all, probing Dataset: NT benchmark Promoter all | 0.672 (± 0.023) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.023 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (large) on NT benchmark Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (large)', column 'Promoter all'; printed identically in Supplementary Table 7 |
| Configuration: BPNet (original), trained from scratch (NT benchmark) | Protocol: NT benchmark Promoter all, probing Dataset: NT benchmark Promoter all | 0.696 (± 0.026) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.026 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (original) on NT benchmark Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (original)', column 'Promoter all'; printed identically in Supplementary Table 7 |
| Configuration: BPNet (X-large), trained from scratch (NT benchmark) | Protocol: NT benchmark Promoter all, probing Dataset: NT benchmark Promoter all | 0.579 (± 0.087) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.087 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (X-large) on NT benchmark Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Promoter all'; printed identically in Supplementary Table 7 |
| Configuration: DNABERT-2, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.754 (± 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 Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'DNABERT-2', column 'Promoter all' |
| Configuration: Enformer, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.745 (± 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 sourceEnformer on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'Enformer', column 'Promoter all' |
| Configuration: HyenaDNA-1KB, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.693 (± 0.016) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.016 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-1KB on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'HyenaDNA-1KB', column 'Promoter all' |
| Configuration: HyenaDNA-32KB, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.698 (± 0.011) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.011 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-32KB on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'HyenaDNA-32KB', column 'Promoter all' |
| Configuration: NT-1000G (2.5B), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.708 (± 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 sourceNT-1000G (2.5B) on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-1000G (2.5B)', column 'Promoter all' |
| Configuration: NT-1000G (2.5B), probing (NT benchmark) | Protocol: NT benchmark Promoter all, probing Dataset: NT benchmark Promoter all | 0.73 (± 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 Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (2.5B)', column 'Promoter all' |
| Configuration: NT-1000G (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.727 (± 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 sourceNT-1000G (500M) on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-1000G (500M)', column 'Promoter all' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark Promoter all, probing Dataset: NT benchmark Promoter all | 0.715 (± 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 Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'Promoter all' |
| Configuration: NT 2.5B Randomly Initialized, trained from scratch (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.589 (± 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 2.5B Randomly Initialized on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT 2.5B Randomly Initialized', column 'Promoter all' |
| Configuration: NT 500M Randomly Initialized, trained from scratch (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.575 (± 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 500M Randomly Initialized on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT 500M Randomly Initialized', column 'Promoter all' |
| Configuration: NT-HumanRef (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.734 (± 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 Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-HumanRef (500M)', column 'Promoter all' |
| Configuration: NT-HumanRef (500M), probing (NT benchmark) | Protocol: NT benchmark Promoter all, probing Dataset: NT benchmark Promoter all | 0.703 (± 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-HumanRef (500M) on NT benchmark Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-HumanRef (500M)', column 'Promoter all' |
| Configuration: NT-Multispecies (2.5B), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.761 (± 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 (2.5B) on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies (2.5B)', column 'Promoter all' |
| Configuration: NT-Multispecies (2.5B), probing (NT benchmark) | Protocol: NT benchmark Promoter all, probing Dataset: NT benchmark Promoter all | 0.743 (± 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 (2.5B) on NT benchmark Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-Multispecies (2.5B)', column 'Promoter all' |
| Configuration: NT-Multispecies-v2 (100M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.753 (± 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-Multispecies-v2 (100M) on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (100M)', column 'Promoter all' |
| Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.774 (± 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 (250M) on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Promoter all' |
| Configuration: NT-Multispecies-v2 (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.778 (± 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-v2 (500M) on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (500M)', column 'Promoter all' |
| Configuration: NT-Multispecies-v2 (50M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all | 0.731 (± 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 (50M) on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (50M)', column 'Promoter all' |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark Promoter all, probing Dataset: NT benchmark Promoter all | 0.598 (± 0.002) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRaw Probe on NT benchmark Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'Raw Probe', column 'Promoter all'; printed identically in Supplementary Table 7 |
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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified
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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 1584 test sequences, maximum length 300 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 Promoter all. 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 Promoter all 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-promoter-all