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Benchmark

Nucleotide Transformer benchmark (18 tasks)

Eighteen human genomic classification tasks (ten histone marks, enhancers, enhancer types, three promoter sets and three splice-site sets) scored by MCC with tenfold cross-validation.

Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.

37 protocols with results

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Methods and evaluation design

Procedure, tasks and evaluated configurations

Baseline coverage

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Baseline status by linked protocol

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

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Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-ntbench-benchmark-nucleotide-transformer-benchmark

areas
dna-genomes
contexts
research
entity level
suite
version
Nature Methods 2025 (Supplementary Table 5)
task
Genomic sequence classification
scope note
Probing (Supplementary Table 6) and parameter-efficient fine-tuning (Supplementary Table 7) of NT models, with DNABERT-2, HyenaDNA, Enformer, BPNet and randomly initialised controls.
source locator
Supplementary Table 5; Supplementary Tables 6, 7 and 9
Related records

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