Raw Probe, probing of raw sequence (NT benchmark)
Raw Probe, probing of raw sequence, a configuration of Raw sequence probe: probing of raw sequence.
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: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark Enhancer, probing Dataset: NT benchmark Enhancer | 0.251 (± 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 sourceRaw Probe 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 'Raw Probe', column 'Enhancer'; printed identically in Supplementary Table 7 |
| 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 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H2AFZ, probing Dataset: NT benchmark H2AFZ | 0.302 (± 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 sourceRaw Probe 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 'Raw Probe', column 'H2AFZ'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H3K27ac, probing Dataset: NT benchmark H3K27ac | 0.229 (± 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 sourceRaw Probe 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 'Raw Probe', column 'H3K27ac'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H3K27me3, probing Dataset: NT benchmark H3K27me3 | 0.379 (± 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 H3K27me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k27me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'Raw Probe', column 'H3K27me3'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H3K36me3, probing Dataset: NT benchmark H3K36me3 | 0.36 (± 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 sourceRaw Probe 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 'Raw Probe', column 'H3K36me3'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H3K4me1, probing Dataset: NT benchmark H3K4me1 | 0.287 (± 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 sourceRaw Probe 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 'Raw Probe', column 'H3K4me1'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H3K4me2, probing Dataset: NT benchmark H3K4me2 | 0.36 (± 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 sourceRaw Probe 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 'Raw Probe', column 'H3K4me2'; printed identically in Supplementary Table 7 |
| 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 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H3K9ac, probing Dataset: NT benchmark H3K9ac | 0.322 (± 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 sourceRaw Probe 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 'Raw Probe', column 'H3K9ac'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H3K9me3, probing Dataset: NT benchmark H3K9me3 | 0.105 (± 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 sourceRaw Probe 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 'Raw Probe', column 'H3K9me3'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark H4K20me1, probing Dataset: NT benchmark H4K20me1 | 0.446 (± 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 sourceRaw Probe 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 'Raw Probe', column 'H4K20me1'; printed identically in Supplementary Table 7 |
| 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 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark Promoter non-TATA, probing Dataset: NT benchmark Promoter non-TATA | 0.619 (± 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 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 'Raw Probe', column 'Promoter non-TATA'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark Promoter TATA, probing Dataset: NT benchmark Promoter TATA | 0.606 (± 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 sourceRaw Probe 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 'Raw Probe', column 'Promoter TATA'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark Splice acceptor, probing Dataset: NT benchmark Splice acceptor | 0.136 (± 0.04) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.04 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRaw Probe 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 'Raw Probe', column 'Splice acceptor'; printed identically in Supplementary Table 7 |
| 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 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark Splice site all, probing Dataset: NT benchmark Splice site all | 0.234 (± 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 sourceRaw Probe 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 'Raw Probe', column 'Splice site all'; printed identically in Supplementary Table 7 |
| Configuration: Raw Probe, probing of raw sequence (NT benchmark) | Protocol: NT benchmark normalised summed performance (Supplementary Table 9) Dataset: NT benchmark, all 18 tasks | 0.391 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 sourceRaw Probe (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 'Raw Probe', 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-raw-probe-probing-of-raw-sequence
- areas
- dna-genomes
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- Raw Probe
- foundation model eligible
- false
- parameters
- probing of raw sequence; hyperparameters in Supplementary Tables 1 and 8
- access reuse
- Not stated in the tables
- 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
- Raw Probe as evaluated in the NT benchmark, probing of raw sequence.
Related records
- configuration of: Raw sequence probe
- system: Raw Probe on NT benchmark Enhancer (probing)
- system: Raw Probe on NT benchmark Enhancer types (probing)
- system: Raw Probe on NT benchmark H2AFZ (probing)
- system: Raw Probe on NT benchmark H3K27ac (probing)
- system: Raw Probe on NT benchmark H3K27me3 (probing)
- system: Raw Probe on NT benchmark H3K36me3 (probing)
- system: Raw Probe on NT benchmark H3K4me1 (probing)
- system: Raw Probe on NT benchmark H3K4me2 (probing)
- system: Raw Probe on NT benchmark H3K4me3 (probing)
- system: Raw Probe on NT benchmark H3K9ac (probing)
- system: Raw Probe on NT benchmark H3K9me3 (probing)
- system: Raw Probe on NT benchmark H4K20me1 (probing)
- system: Raw Probe on NT benchmark Promoter all (probing)
- system: Raw Probe on NT benchmark Promoter non-TATA (probing)
- system: Raw Probe on NT benchmark Promoter TATA (probing)
- system: Raw Probe on NT benchmark Splice acceptor (probing)
- system: Raw Probe on NT benchmark Splice donor (probing)
- system: Raw Probe on NT benchmark Splice site all (probing)
- system: Raw Probe (Probing) NT benchmark normalised summed performance