Result

F1 (NT-splice-sites-donors, fine-tuned) of GENA-LM-large fine-tuned with an appended convolutional layer (You et al. 2026) on Nucleotide Transformer benchmark splice-site dataset, donors

0.9595(0.0005) F1 (NT-splice-sites-donors, fine-tuned)

Methods

Tested configuration: GENA-LM-large fine-tuned with an appended convolutional layer (You et al. 2026)
Protocol: NT-splice-sites-donors splice-site classification, fine-tuned models (You et al. 2026 Supplementary Table 4)
Dataset: Nucleotide Transformer benchmark splice-site dataset, donors
Procedure: NT-splice-sites-donors splice-site classification, fine-tuned models (You et al. 2026 Supplementary Table 4)
Evaluation: GENA-LM-large on NT-splice-sites-donors
Coverage: Not reported scored / Not reported eligible
Uncertainty: SD 0.0005
Evidence: Independent external evaluation · source checkedBenchmarking pre-trained genomic language models for RNA sequence-related predictive applications; You et al. 2026, Supplementary Information · Supplementary Table 4, block 'NT-splice-sites-donors', row 'GENA-LM-large', column 'F1 Score'

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: 19,775 train / 2,198 test
Adaptation: Fine-tuned with an appended convolution head
Scoring implementation: F1 score, precision, recall and accuracy

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

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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.

2 evidence rows 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 0.9595(0.0005) Individual claims	Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications Original source ↗ Supplementary Table 4, block 'NT-splice-sites-donors', row 'GENA-LM-large', column 'F1 Score' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nat Commun 17:223, published online 2025-12-07; PMC12780105 full-text XML Retrieved: 2026-10-11T00:55:34Z	source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit details Independent review 2026-10-11: value and identity match the source. Corrected in review: 500 bp input removed: the source states it for the GTEx task only. Field: `attributes.printed_value` Source artifact SHA-256: `2c6b2816846a21296c56b4dd58f3d1e8810e9d96e224d3ab21b5eb8faa9928e4` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882` Extraction artifact
Reported result 0.9595(0.0005) Individual claims	You et al. 2026, Supplementary Information Original source ↗ Supplementary Table 4, block 'NT-splice-sites-donors', row 'GENA-LM-large', column 'F1 Score' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41467_2025_66899_MOESM1_ESM.pdf inside the Europe PMC supplementaryFiles zip (outer zip 9a0d0a8d8643872ab265e3e6ed7eea944563da4861bf764f97c68fc6aa502525, assembled per request; the member hash is the bound artifact) Retrieved: 2026-10-11T00:55:34Z	source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit details Independent review 2026-10-11: value and identity match the source. Corrected in review: 500 bp input removed: the source states it for the GTEx task only. Field: `attributes.printed_value` Source artifact SHA-256: `cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882` Extraction artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications · Original source · Nat Commun 17:223, published online 2025-12-07; PMC12780105 full-text XML
You et al. 2026, Supplementary Information · Original source · 41467_2025_66899_MOESM1_ESM.pdf inside the Europe PMC supplementaryFiles zip (outer zip 9a0d0a8d8643872ab265e3e6ed7eea944563da4861bf764f97c68fc6aa502525, assembled per request; the member hash is the bound artifact)

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Technical metadata and extraction receipts

Stable ID: gfm2-20261011-you2026-result-t4-nt-splice-donors-gena-lm-large-f1-score

metric: f1-score
metric direction: higher
unit: fraction
printed value: 0.9595(0.0005)
numeric value: 0.9595
source locator: Supplementary Table 4, block 'NT-splice-sites-donors', row 'GENA-LM-large', column 'F1 Score'
metric qualifier: NT-splice-sites-donors, fine-tuned
uncertainty: type: standard_deviation; value: 0.0005; printed: (0.0005); n: 3; scope: Three fine-tuning runs with different random initialisations
review: method: source-hash-verification; pdf-text-parse; independent-cell-check; method note: Re-downloaded the article XML (SHA-256 matches) and the supplementaryFiles zip, whose MOESM1_ESM.pdf member matches the pinned SHA-256. Parsed Supplementary Tables 4 and 5 from the `pdftotext -layout` (poppler 26.08.0) text with a separate parser (review/review.py) and checked printed value, numeric value, spread, metric, qualifier, unit, direction, locator and the linked configuration, protocol and dataset against the block, row and column labels and the article's Methods and Table 1.; reviewer: claude; reviewer note: Claude (Opus 5.5) review agent reviewer-gfm-a, independent of the extractor lit-gfm-2; no human review claimed; date: 2026-10-11; artifact sha256: cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12780105/supplementaryFiles; note: Independent review 2026-10-11: value and identity match the source. Corrected in review: 500 bp input removed: the source states it for the GTEx task only.

Related records

evaluation: GENA-LM-large on NT-splice-sites-donors

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