Evaluation

NucleotideTransformer on the GTEx splicing task, Splice acceptors and donors

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Evaluation results

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: NucleotideTransformer fine-tuned with an appended convolutional layer (You et al. 2026)	Protocol: GTEx tissue-specific splicing prediction, Splice acceptors and donors (You et al. 2026 Supplementary Table 5) Dataset: GTEx-derived tissue-specific splice site usage dataset (You et al. 2026)	0.8826(0.0036) AUPRC (GTEx splicing task, Splice acceptors and donors, averaged over categories) fraction · higher Uncertainty: SD 0.0036 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NucleotideTransformer on the GTEx splicing task, Splice acceptors and donors gfm2-20261011-you2026-protocol-gtex-acceptors-donors Aggregation: Not reported Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications; You et al. 2026, Supplementary Information · Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer', column 'Average PR-AUC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Evaluation procedure

GTEx tissue-specific splicing prediction, Splice acceptors and donors (You et al. 2026 Supplementary Table 5)

Configuration: NucleotideTransformer fine-tuned with an appended convolutional layer (You et al. 2026)
Protocol: GTEx tissue-specific splicing prediction, Splice acceptors and donors (You et al. 2026 Supplementary Table 5)
Dataset: GTEx-derived tissue-specific splice site usage dataset (You et al. 2026)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: gfm2-20261011-you2026-protocol-gtex-acceptors-donors
dataset version: GTEx-derived dataset as constructed by You et al. 2026
split: 242,017 train / 99,813 test
population: Human; 341,830 entries
inputs: 500 bp DNA sequence, scoring all sites in the central 500 bp
adaptation: Fine-tuned with an appended convolution head
metric implementation: Average PR-AUC and average top-k accuracy
aggregation: Mean over three fine-tuning runs
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: 242,017 train / 99,813 test
Adaptation: Fine-tuned with an appended convolution head
Scoring implementation: Average PR-AUC and average top-k accuracy

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Evidence table

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38 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
Comparison: adaptation Fine-tuned with an appended convolution head Context-only references	Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `2c6b2816846a21296c56b4dd58f3d1e8810e9d96e224d3ab21b5eb8faa9928e4` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Fine-tuned with an appended convolution head Context-only references	You et al. 2026, Supplementary Information Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Mean over three fine-tuning runs Context-only references	Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `2c6b2816846a21296c56b4dd58f3d1e8810e9d96e224d3ab21b5eb8faa9928e4` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Mean over three fine-tuning runs Context-only references	You et al. 2026, Supplementary Information Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `2c6b2816846a21296c56b4dd58f3d1e8810e9d96e224d3ab21b5eb8faa9928e4` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	You et al. 2026, Supplementary Information Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version GTEx-derived dataset as constructed by You et al. 2026 Context-only references	Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `2c6b2816846a21296c56b4dd58f3d1e8810e9d96e224d3ab21b5eb8faa9928e4` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version GTEx-derived dataset as constructed by You et al. 2026 Context-only references	You et al. 2026, Supplementary Information Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs 500 bp DNA sequence, scoring all sites in the central 500 bp Context-only references	Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `2c6b2816846a21296c56b4dd58f3d1e8810e9d96e224d3ab21b5eb8faa9928e4` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs 500 bp DNA sequence, scoring all sites in the central 500 bp Context-only references	You et al. 2026, Supplementary Information Original source ↗ Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer' 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	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `cbb69e05045a4526e35479d2c1361ebb9cfadfd968e00675390dad597035d882` Hash scope: Hash scope not separately documented; inspect source record Inspected 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-eval-t5-acceptors-donors-nucleotidetransformer

areas: dna-genomes
contexts: research
origin: independent_paper
protocol: gfm2-20261011-you2026-protocol-gtex-acceptors-donors
version: Primary source as retrieved 2026-10-11
comparison: protocol id: gfm2-20261011-you2026-protocol-gtex-acceptors-donors; dataset version: GTEx-derived dataset as constructed by You et al. 2026; split: 242,017 train / 99,813 test; population: Human; 341,830 entries; inputs: 500 bp DNA sequence, scoring all sites in the central 500 bp; adaptation: Fine-tuned with an appended convolution head; metric implementation: Average PR-AUC and average top-k accuracy; aggregation: Mean over three fine-tuning runs; budget: Not reported
source locator: Supplementary Table 5, block 'Splice acceptors and donors', row 'NucleotideTransformer'
limitations: Fine-tuned and tested three times with different random initialisations; the printed spread is the standard deviation over those three runs (Methods, 'To ensure the reliability of our findings').; All methods are given a 500 bp input so that models with different context windows are comparable; SpTransformer and SpliceAI were designed for 1,000 to 5,000 nucleotide inputs (Results).; Each language model is fine-tuned with an appended convolution head, so the comparison measures the adapted model, not zero-shot likelihood.; Values are read from the Supplementary Information tables behind the figures; the main-text figures are not read.

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