Nucleotide Transformer downstream task Splice donor.
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 Splice donor, probing Dataset: NT benchmark Splice donor | 0.93 (± 0.021) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.021 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (large) on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (large)', column 'Splice donor'; printed identically in Supplementary Table 7 |
| Configuration: BPNet (original), trained from scratch (NT benchmark) | Protocol: NT benchmark Splice donor, probing Dataset: NT benchmark Splice donor | 0.92 (± 0.014) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.014 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBPNet (original) on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (original)', column 'Splice donor'; printed identically in Supplementary Table 7 |
| Configuration: BPNet (X-large), trained from scratch (NT benchmark) | Protocol: NT benchmark Splice donor, probing Dataset: NT benchmark Splice donor | 0.706 (± 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 sourceBPNet (X-large) on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Splice donor'; printed identically in Supplementary Table 7 |
| Configuration: DNABERT-2, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.861 (± 0.004) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.004 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'DNABERT-2', column 'Splice donor' |
| Configuration: Enformer, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.78 (± 0.007) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.007 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'Enformer', column 'Splice donor' |
| Configuration: HyenaDNA-1KB, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.943 (± 0.024) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.024 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-1KB on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'HyenaDNA-1KB', column 'Splice donor' |
| Configuration: HyenaDNA-32KB, parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.915 (± 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 sourceHyenaDNA-32KB on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'HyenaDNA-32KB', column 'Splice donor' |
| Configuration: NT-1000G (2.5B), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.963 (± 0.001) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G (2.5B) on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-1000G (2.5B)', column 'Splice donor' |
| Configuration: NT-1000G (2.5B), probing (NT benchmark) | Protocol: NT benchmark Splice donor, probing Dataset: NT benchmark Splice donor | 0.621 (± 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 (2.5B) on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (2.5B)', column 'Splice donor' |
| Configuration: NT-1000G (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.952 (± 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 Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-1000G (500M)', column 'Splice donor' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark Splice donor, probing Dataset: NT benchmark Splice donor | 0.542 (± 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-1000G (500M) on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'Splice donor' |
| Configuration: NT 2.5B Randomly Initialized, trained from scratch (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.641 (± 0.045) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.045 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT 2.5B Randomly Initialized on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT 2.5B Randomly Initialized', column 'Splice donor' |
| Configuration: NT 500M Randomly Initialized, trained from scratch (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.596 (± 0.057) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.057 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT 500M Randomly Initialized on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT 500M Randomly Initialized', column 'Splice donor' |
| Configuration: NT-HumanRef (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.952 (± 0.003) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-HumanRef (500M) on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-HumanRef (500M)', column 'Splice donor' |
| Configuration: NT-HumanRef (500M), probing (NT benchmark) | Protocol: NT benchmark Splice donor, probing Dataset: NT benchmark Splice donor | 0.495 (± 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-HumanRef (500M) on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-HumanRef (500M)', column 'Splice donor' |
| Configuration: NT-Multispecies (2.5B), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.97 (± 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 sourceNT-Multispecies (2.5B) on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies (2.5B)', column 'Splice donor' |
| Configuration: NT-Multispecies (2.5B), probing (NT benchmark) | Protocol: NT benchmark Splice donor, probing Dataset: NT benchmark Splice donor | 0.687 (± 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-Multispecies (2.5B) on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-Multispecies (2.5B)', column 'Splice donor' |
| Configuration: NT-Multispecies-v2 (100M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.947 (± 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-Multispecies-v2 (100M) on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (100M)', column 'Splice donor' |
| Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.967 (± 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-Multispecies-v2 (250M) on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Splice donor' |
| Configuration: NT-Multispecies-v2 (500M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.96 (± 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 (500M) on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (500M)', column 'Splice donor' |
| Configuration: NT-Multispecies-v2 (50M), parameter-efficient fine-tuning (NT benchmark) | Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor | 0.915 (± 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 Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (50M)', column 'Splice donor' |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark Splice donor, probing Dataset: NT benchmark Splice donor | 0.395 (± 0.025) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.025 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRaw Probe on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'Raw Probe', column 'Splice donor'; 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 600 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 Splice donor. 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 Splice donor 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-splice-donor