Result

MCC (median over 10 cross-validation folds) of Enformer, parameter-efficient fine-tuning (NT benchmark) on NT benchmark H3K4me2

0.626 (± 0.015) MCC (median over 10 cross-validation folds)

Methods

Tested configuration: Enformer, parameter-efficient fine-tuning (NT benchmark)
Protocol: NT benchmark H3K4me2, fine-tuning (PEFT)
Dataset: NT benchmark H3K4me2
Procedure: NT benchmark H3K4me2, fine-tuning (PEFT)
Evaluation: Enformer on NT benchmark H3K4me2 (fine-tuning)
Coverage: Not reported scored / Not reported eligible
Uncertainty: SD 0.015
Evidence: Independent external evaluation · source checkedNucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'Enformer', column 'H3K4me2'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Tenfold cross-validation
Adaptation: parameter-efficient fine-tuning
Scoring implementation: MCC

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Reported result 0.626 (± 0.015) Individual claims	Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) Original source ↗ Supplementary Table 7, row 'Enformer', column 'H3K4me2' Version: Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages) Retrieved: 2026-10-11T01:37:37Z	source checked ["source-hash-verification","pdf-text-parse","independent-cell-check","rendered-source-visual-check"] · 2026-10-11 independent paper Audit details Extraction: Parsed the pdftotext -layout text of the pinned Supplementary Information PDF with tools/extract_ntbench.py: each block's 'Dataset' header gives six task columns, model rows matched as label followed by six 'value (± sd)' cells; block, row and column counts asserted. Supplementary Table 7, row 'Enformer', column 'H3K4me2' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md. Field: `attributes.printed_value` Source artifact SHA-256: `ef0f357a1289aad1910059d455579e242a9a82ab3e32ec38d8ea2584effc436e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `ef0f357a1289aad1910059d455579e242a9a82ab3e32ec38d8ea2584effc436e` Extraction artifact

How to read the evidence

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)

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-ntbench-result-enformer-fine-tuning-h3k4me2

metric: matthews-correlation-coefficient
metric direction: higher
unit: unitless
printed value: 0.626 (± 0.015)
source locator: Supplementary Table 7, row 'Enformer', column 'H3K4me2'
review: method: source-hash-verification; pdf-text-parse; independent-cell-check; rendered-source-visual-check; method note: Matched the re-downloaded Supplementary Information PDF's SHA-256; an independent parser over the text layer compared all values (printed, numeric and SD) with 0 mismatches; a seeded stratified sample of 62 cells was checked against rendered pages 7 and 8.; reviewer: claude; reviewer note: Claude review agent reviewer-gen-2, independent of the extractor lit-genomics; no human review claimed; date: 2026-10-11; artifact sha256: ef0f357a1289aad1910059d455579e242a9a82ab3e32ec38d8ea2584effc436e; retrieval url: https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-024-02523-z/MediaObjects/41592_2024_2523_MOESM1_ESM.pdf; note: Extraction: Parsed the pdftotext -layout text of the pinned Supplementary Information PDF with tools/extract_ntbench.py: each block's 'Dataset' header gives six task columns, model rows matched as label followed by six 'value (± sd)' cells; block, row and column counts asserted. Supplementary Table 7, row 'Enformer', column 'H3K4me2' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md.
numeric value: 0.626
metric qualifier: median over 10 cross-validation folds
uncertainty: type: standard_deviation; value: 0.015; printed: ± 0.015; scope: across 10 cross-validation folds; n: 10

Related records

evaluation: Enformer on NT benchmark H3K4me2 (fine-tuning)

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