Evaluation

Nucleotide Transformer on RNAGym v0.1.1 fitness (tRNA)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Nucleotide Transformer (RNAGym fitness leaderboard v0.1.1)	Protocol: RNAGym v0.1.1 fitness, signed Spearman, tRNA Dataset: RNAGym tRNA DMS assays (3)	0.317 Spearman (mean signed Spearman over the 3 tRNA assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Nucleotide Transformer on RNAGym v0.1.1 fitness (tRNA) lit-rna-20261011-rnagym-protocol-signed-spearman-trna Aggregation: Not reported RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md · leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)'

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

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

RNAGym v0.1.1 fitness, signed Spearman, tRNA

Configuration: Nucleotide Transformer (RNAGym fitness leaderboard v0.1.1)
Protocol: RNAGym v0.1.1 fitness, signed Spearman, tRNA
Dataset: RNAGym tRNA DMS assays (3)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: lit-rna-20261011-rnagym-protocol-signed-spearman-trna
dataset version: RNAGym v0.1.1
split: Whole assays (zero-shot)
population: Not reported
inputs: Wild-type and variant RNA sequences
adaptation: Zero-shot; masked-marginal log-likelihood ratio for masked language models
metric implementation: Signed Spearman (performance_fitness.py --type ncRNA on branch v0.2)
aggregation: Mean over assays in the category
budget: Not reported

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

Reproduction

Split: Whole assays (zero-shot)
Adaptation: Zero-shot; masked-marginal log-likelihood ratio for masked language models
Scoring implementation: Signed Spearman (performance_fitness.py --type ncRNA on branch v0.2)

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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

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19 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 Zero-shot; masked-marginal log-likelihood ratio for masked language models Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Mean over assays in the category Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version RNAGym v0.1.1 Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Wild-type and variant RNA sequences Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: metric implementation Signed Spearman (performance_fitness.py --type ncRNA on branch v0.2) Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: population Not reported Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: protocol id lit-rna-20261011-rnagym-protocol-signed-spearman-trna Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: split Whole assays (zero-shot) Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 1 values Run by the RNAGym maintainers with their scoring scripts, not by the model developers. Context-only references	RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md Original source ↗ leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)' Version: Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1 Retrieved: 2026-10-11T21:40:04Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.limitations` Source artifact SHA-256: `c947a7a45a53cc4106323a3bcae1bb3fa84276bc07df89493cb501735711b891` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

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

1 source record and release history

RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md · Original source · Commit 2828cf99316d75daaa8d832a2573cbb25bbd35fe (2026-08-14, 'Update fitness leaderboard v0.2 models'); leaderboard labelled v0.1.1

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Technical metadata and extraction receipts

Stable ID: lit-rna-20261011-rnagym-eval-nucleotide-transformer-trna

areas: rna-transcriptomes
contexts: research
origin: independent_paper
protocol: lit-rna-20261011-rnagym-protocol-signed-spearman-trna
version: Primary source as retrieved 2026-10-11
comparison: protocol id: lit-rna-20261011-rnagym-protocol-signed-spearman-trna; dataset version: RNAGym v0.1.1; split: Whole assays (zero-shot); population: Not reported; inputs: Wild-type and variant RNA sequences; adaptation: Zero-shot; masked-marginal log-likelihood ratio for masked language models; metric implementation: Signed Spearman (performance_fitness.py --type ncRNA on branch v0.2); aggregation: Mean over assays in the category; budget: Not reported
source locator: leaderboard/fitness/README.md, main leaderboard table, row 'Nucleotide Transformer', column 'tRNA (n=3)'
missing metadata: comparison.budget: reason: unreported; comparison.population: reason: unreported
limitations: Run by the RNAGym maintainers with their scoring scripts, not by the model developers.

Related records

system: Nucleotide Transformer (RNAGym fitness leaderboard v0.1.1)
assessment: RNAGym v0.1.1 fitness, signed Spearman, tRNA
data: RNAGym tRNA DMS assays (3)
evaluation: Nucleotide Transformer RNAGym tRNA signed Spearman

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