Task

translation-efficiency prediction

Translation-efficiency assessment uses published full-transcript measurements and is distinct from the paper’s CDS-only tasks.

Sources

mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table

1 evaluation · 1 metric row

At a glance

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Datasets	PERSIST-seq full-length mRNA measurements and a ribosome-profiling atlas of human/mouse translation efficiency. Sources mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table
Splits	The supplementary full-length section distinguishes PERSIST-seq traits from the human/mouse TE atlas, but gives no TE-atlas train/validation/test membership or partition rule. Five-fold reporting for PERSIST-seq or other downstream tasks cannot be assigned to the atlas result. · Not reported in inspected sources Sources (2) mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset; mrnabert journal Supplementary Information — pinned PDF · Main full-length mRNA results/Methods; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13
Metrics	R-squared and Spearman correlation for the human/mouse translation-efficiency atlas; separate mRNA tasks use their own metrics. Sources mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table
Baselines	Comparison models are fine-tuned using a common model library for the full-length mRNA task. Sources mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table
Leakage controls	The main and supplementary TE-atlas descriptions provide sequence-length and dataset summaries but do not describe exclusion of homologous transcripts, shared genes or pretraining overlap for that experiment. Controls described for other downstream datasets are not atlas controls. · Not reported in inspected sources Sources (2) mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset; mrnabert journal Supplementary Information — pinned PDF · Methods: translation efficiency; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13
Uncertainty	The TE-atlas comparison has no task-specific repeat count or confidence-interval method in the inspected main and supplementary sections. The five-fold means/standard deviations for the separate PERSIST-seq evaluation do not define atlas uncertainty. · Not reported in inspected sources Sources (2) mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset; mrnabert journal Supplementary Information — pinned PDF · Main TE-atlas results; Supplementary Information Full-Length mRNA, pp19–21
Entity type	Paper-specific computational evaluation protocol. Sources mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table
Organisms	Human and mouse. Sources mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table
Assays	PERSIST-seq and ribosome-profiling translation-efficiency measurements. Sources mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table
Allowed inputs	Full-length mRNA sequence. Sources mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table
Adaptation	Task fine-tuning through a common comparison-model library. Sources mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table

How it works

How it worksComputational evaluation flow

Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.

Sources

Evaluation methodology

PERSIST-seq full-length mRNA measurements and a ribosome-profiling atlas of human/mouse translation efficiency. R-squared and Spearman correlation for the human/mouse translation-efficiency atlas; separate mRNA tasks use their own metrics. Comparison models are fine-tuned using a common model library for the full-length mRNA task.

Sources

Recorded evaluations

Each evaluation records what was tested and under which conditions.

mRNABERT: translation-efficiency prediction

Tested entities and results

Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
mRNABERT: translation-efficiency prediction Configuration: mRNABERTTask: translation-efficiency predictionDataset: human ultra-long mRNAs human translation-efficiency regression at 3066-nt input Author-reported evaluation · Evaluation metadata: needs review
0.669 R-squared Unit: unitless · Direction: unknown	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Table 2, mRNABERT (3066) row, Human R-squared column Source checking is not independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.

Paper or primary resource	Version	Reference
mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset	journal full text in PMC	Read source

What is still missing

complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.
exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.

Search and extraction details

primary comparison tables located

Searches

mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset 10.1038/s41467-025-65340-8

Evidence locations

Table 1; XML table Tab1
Table 2; XML table Tab2

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

PERSIST-seq full-transcript traits and the human/mouse TE atlas are different evaluations. The supplementary section identifies them separately but does not supply an atlas partition or uncertainty protocol.
Sources (2)
mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset; mrnabert journal Supplementary Information — pinned PDF · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table ; Supplementary Information task sections

What remains unknown

Splits: The supplementary full-length section distinguishes PERSIST-seq traits from the human/mouse TE atlas, but gives no TE-atlas train/validation/test membership or partition rule. Five-fold reporting for PERSIST-seq or other downstream tasks cannot be assigned to the atlas result.
Leakage controls: The main and supplementary TE-atlas descriptions provide sequence-length and dataset summaries but do not describe exclusion of homologous transcripts, shared genes or pretraining overlap for that experiment. Controls described for other downstream datasets are not atlas controls.
Uncertainty: The TE-atlas comparison has no task-specific repeat count or confidence-interval method in the inspected main and supplementary sections. The five-fold means/standard deviations for the separate PERSIST-seq evaluation do not define atlas uncertainty.

Profile review details

Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.

Stable record: reported-task-f7142c3b3e0f3c

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.

21 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims	mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Original source ↗ Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558216+00:00	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `ff08ba895b7080446c08a930548b48a0041ae990c222ebb07e6ba7dcaf48ad44` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps ["Input: Full-length mRNA sequence.","Evaluation: Task fine-tuning through a common comparison-model library.","Readout: R-squared and Spearman correlation for the human/mouse translation-efficiency atlas; separate mRNA tasks use their own metrics."] Individual claims	mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Original source ↗ Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558216+00:00	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `ff08ba895b7080446c08a930548b48a0041ae990c222ebb07e6ba7dcaf48ad44` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Computational evaluation flow Individual claims	mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Original source ↗ Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558216+00:00	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `ff08ba895b7080446c08a930548b48a0041ae990c222ebb07e6ba7dcaf48ad44` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Datasets PERSIST-seq full-length mRNA measurements and a ribosome-profiling atlas of human/mouse translation efficiency. Individual claims	mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Original source ↗ Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558216+00:00	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `ff08ba895b7080446c08a930548b48a0041ae990c222ebb07e6ba7dcaf48ad44` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Splits The supplementary full-length section distinguishes PERSIST-seq traits from the human/mouse TE atlas, but gives no TE-atlas train/validation/test membership or partition rule. Five-fold reporting for PERSIST-seq or other downstream tasks cannot be assigned to the atlas result. Individual claims	mrnabert journal Supplementary Information — pinned PDF Original source ↗ Main full-length mRNA results/Methods; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published supplementary PDF 41467_2025_65340_MOESM1_ESM.pdf; sha256:2820d9385389e41e9213223608b26c84bf6bffbba57ff48fd5dda17fb78a8aed Retrieved: 2026-09-16T21:06:12.558631+00:00	unreported automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `2820d9385389e41e9213223608b26c84bf6bffbba57ff48fd5dda17fb78a8aed` Hash scope: Hash scope not separately documented; inspect source record Archive member: 41467_2025_65340_MOESM1_ESM.pdf Inspected artifact
Splits The supplementary full-length section distinguishes PERSIST-seq traits from the human/mouse TE atlas, but gives no TE-atlas train/validation/test membership or partition rule. Five-fold reporting for PERSIST-seq or other downstream tasks cannot be assigned to the atlas result. Individual claims	mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Original source ↗ Main full-length mRNA results/Methods; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558216+00:00	unreported automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `ff08ba895b7080446c08a930548b48a0041ae990c222ebb07e6ba7dcaf48ad44` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Adaptation Task fine-tuning through a common comparison-model library. Individual claims	mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Original source ↗ Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558216+00:00	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `ff08ba895b7080446c08a930548b48a0041ae990c222ebb07e6ba7dcaf48ad44` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Metrics R-squared and Spearman correlation for the human/mouse translation-efficiency atlas; separate mRNA tasks use their own metrics. Individual claims	mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Original source ↗ Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558216+00:00	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `ff08ba895b7080446c08a930548b48a0041ae990c222ebb07e6ba7dcaf48ad44` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Baselines Comparison models are fine-tuned using a common model library for the full-length mRNA task. Individual claims	mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Original source ↗ Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558216+00:00	source checked automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `ff08ba895b7080446c08a930548b48a0041ae990c222ebb07e6ba7dcaf48ad44` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Leakage controls The main and supplementary TE-atlas descriptions provide sequence-length and dataset summaries but do not describe exclusion of homologous transcripts, shared genes or pretraining overlap for that experiment. Controls described for other downstream datasets are not atlas controls. Individual claims	mrnabert journal Supplementary Information — pinned PDF Original source ↗ Methods: translation efficiency; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published supplementary PDF 41467_2025_65340_MOESM1_ESM.pdf; sha256:2820d9385389e41e9213223608b26c84bf6bffbba57ff48fd5dda17fb78a8aed Retrieved: 2026-09-16T21:06:12.558631+00:00	unreported automated source review · 2026-09-16 Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `2820d9385389e41e9213223608b26c84bf6bffbba57ff48fd5dda17fb78a8aed` Hash scope: Hash scope not separately documented; inspect source record Archive member: 41467_2025_65340_MOESM1_ESM.pdf Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

3 source records and release history

mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Original source · journal full text in PMC
mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Original source · journal full text in PMC
mrnabert journal Supplementary Information — pinned PDF · Original source · Published supplementary PDF 41467_2025_65340_MOESM1_ESM.pdf; sha256:2820d9385389e41e9213223608b26c84bf6bffbba57ff48fd5dda17fb78a8aed

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Technical metadata and extraction receipts

Stable ID: reported-task-f7142c3b3e0f3c

areas: rna-transcriptomes
tasks: translation-efficiency prediction
entity level: task
version: Not reported
task: translation-efficiency prediction
scope note: Paper-specific evaluation task; protocol completeness requires further extraction.
benchmark research: review date: 2026-09-17; status: primary_comparison_tables_located; primary sources: evidence-expansion-mrnabert-2025-ff08ba89; inspected locators: Table 1; XML table Tab1; Table 2; XML table Tab2; searched queries: mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset 10.1038/s41467-025-65340-8; gaps: complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.; exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
historical missing metadata: protocol version: not_reported_in_legacy_extract
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: mrnabert-2025; source locator: Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.

Related records

dataset: human ultra-long mRNAs
benchmark: mRNABERT: translation-efficiency prediction

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