NT-1000G (500M), probing (NT benchmark)
NT-1000G (500M), probing, a configuration of Nucleotide Transformer: probing.
Overview
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Evaluations and results
19 evaluations · 19 results. Different protocols are not a single leaderboard.
Sorted by MCC (median over 10 cross-validation folds) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 19 result rows with coverage, uncertainty and sources
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark Enhancer, probing Dataset: NT benchmark Enhancer | 0.47 (± 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 (500M) on NT benchmark Enhancer (probing) lit-genomics-20261011-ntbench-protocol-enhancer-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'Enhancer' |
| 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-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H2AFZ, probing Dataset: NT benchmark H2AFZ | 0.404 (± 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 (500M) on NT benchmark H2AFZ (probing) lit-genomics-20261011-ntbench-protocol-h2afz-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H2AFZ' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H3K27ac, probing Dataset: NT benchmark H3K27ac | 0.437 (± 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-1000G (500M) on NT benchmark H3K27ac (probing) lit-genomics-20261011-ntbench-protocol-h3k27ac-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H3K27ac' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H3K27me3, probing Dataset: NT benchmark H3K27me3 | 0.535 (± 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-1000G (500M) on NT benchmark H3K27me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k27me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H3K27me3' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H3K36me3, probing Dataset: NT benchmark H3K36me3 | 0.509 (± 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 H3K36me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k36me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H3K36me3' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H3K4me1, probing Dataset: NT benchmark H3K4me1 | 0.438 (± 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-1000G (500M) on NT benchmark H3K4me1 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me1-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H3K4me1' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H3K4me2, probing Dataset: NT benchmark H3K4me2 | 0.515 (± 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-1000G (500M) on NT benchmark H3K4me2 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me2-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H3K4me2' |
| 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-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H3K9ac, probing Dataset: NT benchmark H3K9ac | 0.523 (± 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 (500M) on NT benchmark H3K9ac (probing) lit-genomics-20261011-ntbench-protocol-h3k9ac-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H3K9ac' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H3K9me3, probing Dataset: NT benchmark H3K9me3 | 0.381 (± 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-1000G (500M) on NT benchmark H3K9me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k9me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H3K9me3' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark H4K20me1, probing Dataset: NT benchmark H4K20me1 | 0.622 (± 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 (500M) on NT benchmark H4K20me1 (probing) lit-genomics-20261011-ntbench-protocol-h4k20me1-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'H4K20me1' |
| 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-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark Promoter non-TATA, probing Dataset: NT benchmark Promoter non-TATA | 0.732 (± 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 (500M) on NT benchmark Promoter non-TATA (probing) lit-genomics-20261011-ntbench-protocol-promoter-non-tata-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'Promoter non-TATA' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark Promoter TATA, probing Dataset: NT benchmark Promoter TATA | 0.696 (± 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 (500M) on NT benchmark Promoter TATA (probing) lit-genomics-20261011-ntbench-protocol-promoter-tata-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'Promoter TATA' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark Splice acceptor, probing Dataset: NT benchmark Splice acceptor | 0.552 (± 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-1000G (500M) on NT benchmark Splice acceptor (probing) lit-genomics-20261011-ntbench-protocol-splice-acceptor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'Splice acceptor' |
| 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-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark Splice site all, probing Dataset: NT benchmark Splice site all | 0.355 (± 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 site all (probing) lit-genomics-20261011-ntbench-protocol-splice-site-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'NT-1000G (500M)', column 'Splice site all' |
| Configuration: NT-1000G (500M), probing (NT benchmark) | Protocol: NT benchmark normalised summed performance (Supplementary Table 9) Dataset: NT benchmark, all 18 tasks | 0.583 MCC (mean over three task categories of median cross-validation MCC) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G (500M) (Probing) NT benchmark normalised summed performance lit-genomics-20261011-ntbench-protocol-normalised-summed-performance Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 9, row 'NT-1000G (500M)', approach 'Probing', column 'Average performance' |
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Original source · Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages)
Technical metadata and extraction receipts
Stable ID: lit-genomics-20261011-ntbench-config-nt-1000g-500m-probing
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- NT-1000G (500M)
- foundation model eligible
- true
- parameters
- probing; hyperparameters in Supplementary Tables 1 and 8
- access reuse
- Public weights (Hugging Face InstaDeepAI collection)
- source locator
- Supplementary Tables 6, 7 and 9 row labels
- missing metadata
- version: reason: unreported; note: Row label gives training data and parameter count only
- provenance note
- NT-1000G (500M) as evaluated in the NT benchmark, probing.
Related records
- configuration of: Nucleotide Transformer
- system: NT-1000G (500M) on NT benchmark Enhancer (probing)
- system: NT-1000G (500M) on NT benchmark Enhancer types (probing)
- system: NT-1000G (500M) on NT benchmark H2AFZ (probing)
- system: NT-1000G (500M) on NT benchmark H3K27ac (probing)
- system: NT-1000G (500M) on NT benchmark H3K27me3 (probing)
- system: NT-1000G (500M) on NT benchmark H3K36me3 (probing)
- system: NT-1000G (500M) on NT benchmark H3K4me1 (probing)
- system: NT-1000G (500M) on NT benchmark H3K4me2 (probing)
- system: NT-1000G (500M) on NT benchmark H3K4me3 (probing)
- system: NT-1000G (500M) on NT benchmark H3K9ac (probing)
- system: NT-1000G (500M) on NT benchmark H3K9me3 (probing)
- system: NT-1000G (500M) on NT benchmark H4K20me1 (probing)
- system: NT-1000G (500M) on NT benchmark Promoter all (probing)
- system: NT-1000G (500M) on NT benchmark Promoter non-TATA (probing)
- system: NT-1000G (500M) on NT benchmark Promoter TATA (probing)
- system: NT-1000G (500M) on NT benchmark Splice acceptor (probing)
- system: NT-1000G (500M) on NT benchmark Splice donor (probing)
- system: NT-1000G (500M) on NT benchmark Splice site all (probing)
- system: NT-1000G (500M) (Probing) NT benchmark normalised summed performance